Horizontal alignment of 5' -> 3' intergene distance segment tropy with respect to the gene as the conserved basis for DNA transcription.

AIM: To study the conserved basis for gene expression in comparative cell types at opposite ends of the cell pressuromodulation spectrum, the lymphatic endothelial cell and the blood microvascular capillary endothelial cell.
METHODS: The mechanism for gene expression is studied in terms of the 5' -> 3' direction paired point tropy quotients (prpTQs) and the final 5' -> 3' direction episodic sub-episode block sums split-integrated weighted average-averaged gene overexpression tropy quotient (esebssiwaagoTQ).
RESULTS: The final 5' -> 3' esebssiwaagoTQ classifies an lymphatic endothelial cell overexpressed gene as a supra-pressuromodulated gene (esebssiwaagoTQ ≥ 0.25 < 0.75) every time and classifies a blood microvascular capillary endothelial cell overexpressed gene every time as an infra-pressuromodulated gene (esebssiwaagoTQ < 0.25) (100% sensitivity; 100% specificity).
CONCLUSION: Horizontal alignment of 5' -> 3' intergene distance segment tropy wrt the gene is the basis for DNA transcription in the pressuromodulated state.

In the biological system in the physiologic state in vivo, water flux across cell membrane channels in response to changes in system osmoregulators (extracellular sodium, intracellular potassium and extracellular and intracellular glucose) maintains baseline biological system osmotic pressure and turgor; however, water flux in response to osmoregulators is not a specific regulator of intracellular pressure as it is a concomitant regulator of both extracellular and intracellular pressure of the biological system.

During the blastocyst-to-gastrula-to-neuralation developmental stages, macropressurization occurs, the mesoderm is subject to the most macropressurization (least intra-cellularly pressurized cells), the endoderm is subject to intermediate macropressurization (intermediately intracellularly pressurized cells) and the ectoderm is subject to the least macropressurization (most intracellularly pressurized cells), as a result of which the baseline densities (g/cm3) of the respective germ layers are set. In the case of the ectoderm, there is the development of the cerebrospinal fluid (CSF) suspended buoyant CNS tissue, which begins as the least dense tissue initially containing the most intracellularly pressurized cells that sprout extensively over long distances after which nuclear pressure decreases substantially resulting in non-dividing neuronal cells (less intracellularly pressurized cells) that further differentiate into specific neuron populations (i.e., acetylcholinergic, glutaminergic, γ-aminobutyric acid, dopaminergic, serotonergic) in response to local microenvironment growth factors [1]. This is analogous to cells in vitro, when cultured cells are in the proliferative phase at approximately 30% confluence {relatively greater intracellularly pressurized cells, as intracellular pressure is much greater [>>>] than extra-cellular} due to lesser cell-to-cell contact, but are in the non-proliferative phase at approximately 80% confluence {relatively lesser intracellularly pressurized cells, as intracellular pressure is only greater [>] extra-cellular} due to greater cell-to-cell contact, as it has been observed by the atomic force microscopy (AFM) that the Young's modulus (kPa) of cells decreases with increasing E-cadherin micro-bead cell contact surface area (relatively less intracellular pressure with increasing cell contact extracellular pressure) [2].

Cells grown in culture are subject only to atmospheric pressure (i.e. 760 mmHg), however the pressure that cells are subject to in vivo is much greater than circulatory blood pressure (i.e. 120/80 mmHg) and greater than atmospheric pressure, as true biological system pressure is the force per unit area (kPa) that cells are actually subject to in vivo, as there is pulsatile pressure through inter-endothelial or inter-epithelial junction open cross-sectional surface area in the pressurized biological system in vivo. Support of this supposition comes from two observations of cell macropressurization at extreme ends of the cell macropressurization spectrum:

The least, when under atmospheric pressure decreasing underlying substrate stiffness (decreasing stiffness of gel substrate by decreasing cross-linking) [3-5] results in decreased cell proliferation [6] as overall extracellular pressure (atmospheric pressure and substrate pressure) decreases below that of the lowest level of biologically possible macropressurization, which can only be rescued by growth factors [7]; as opposed to

The greatest, when stiff microcapsule-encapsulation [8] or in situ application of neoplastic-level stiff intra-ductal pressure to isolated acini [9] results in intimately apposed-and-juxtaposed cell membrane stiffness, actually increases intracellular pressure [10] and results in cell proliferation [8].

These observations taken together imply that:

In the pressurized biological state in vivo, normal attached tissue cells are relatively less pressurized cells in comparison to normal free moving circulatory cells that are relatively more pressurized cells (i.e., tri-lobed nucleus neutrophils > bi-lobed nucleus eosinophils > mono-lobed nucleus cells, among others); and that

In the pressurized biological state in vivo, there are relative decreases in the effectiveness of growth factors, particularly in the effectiveness of lesser potency growth factors [11].

Building on these observations, it has been recently described that cell membrane pressuromodulation, defined as alterations in cell compliance in response cell membrane pressuromodulators {ΔP [mmHg]/ΔV [cm3]}, where the change in cell volume ΔV (Δ cm3) is miniscule (∼constant) as compared with the change in intracellular pressure (ΔP), Ppostpressuromodulator – Ppre-pressuromodulator (Δ mmHg), whereby alterations in cell compliance in response to cell membrane pressuromodulators could by assessed vis a vis the Young's modulus {Force/Area [kPa]/ΔLength/Length initial (ratio); kPa} [12], as the Young's modulus is a measure of cell membrane compliance and would serve as a surrogate measure of changes in cell compliance itself. Cell membrane pressuromodulation plays the pivotal role in the specific regulation of cellular and nuclear function [13-15], via:

Direct cell membrane pressuromodulator without oxidative stress-mediated decrease in cell membrane compliance and increase in intracellular pressure, which favors cell differentiation toward pluripotency, and cell division or cell mitogenic multi-nucleation, for example, as is the case for aldosterone (number of mineralocorticoid receptors: 169 per cell; K D = 0.52 × 10-10 with t 1/2 @ receptor: 140 min) [16-20], for dihydrotestosterone/testosterone (< number of receptors) [21-23], for 17β-estradiol [24,25], for TGF-β1 [22], for HGF/SF [26,27], for IL-1α/β [25,28], for EGF [25], for bFGF [29], for PTH/PTHrP [27], for VEGF (2+ endocytic) [30,31], for phorbol of 12-myristate 13-acetate (PMA, TPA; hydroxylo-, carbonylo- endocytic)[25,32-33], and for dynamic stress/strain [34]; via

Direct cell membrane pressuromodulator with oxidative stress-mediated increase in cell membrane compliance and decrease in intracellular pressure, which favors cell differentiation away from pluripotency, for example, as is the case for dexamethasone (number of glucocorticoid receptors: 1322 per cell; K D = 3.7 × 10-9 with t 1/2 @ receptor: 100 min; > number of receptor-mediated oxidative stress) [16-17,28,30], for dihydrotestosterone/testosterone (> number of receptors; > number of receptor-mediated oxidative stress) [35], and for GM-CSF/CSF-1 (receptor-mediated oxidative stress) [36-38]); and via

Indirect cell membrane pressuromodulator with bilayer cholesterol removal without oxidative stress-mediated decrease in cell membrane compliance and increase in intracellular pressure, which favors cell differentiation toward pluripotency, and cell division or cell mitogenic multi-nucleation, for example, as is the case for ketoconazole [39];

Indirect cell membrane pressuromodulator with esterase activity-related oxidative stress-mediated increase in cell membrane compliance and decrease in intracellular pressure, which favors cell differentiation away from pluripotency, for example, as is the case for 12-myristate and 13-acetate of phorbol 12-myristate 13-acetate (PMA, TPA) [30,33,40]; and

Indirect cell membrane pressuromodulator with bilayer pertubation-mediated increase in cell membrane compliance and decrease in intracellular pressure, which also favors cell differentiation away from pluripotency, for example, as is the case for tocopherols [41,42], for calcifidiol [41,43], and for retinoic acid [43,44].

Even as the various forms of cell membrane pressuromodulation have been shown to be important in the regulation of cellular and nuclear function, an aspect that remains poorly understood is the conserved basis for cellular pressuromodulation state-dependent DNA transcription, which can be understood based on knowledge of the following four knowns for DNA transcription:

The direction of RNA polymerase-dependent DNA transcription is 5′ -> 3′ for both helix (+) and (-) strand transcription;

Genes are transcribable series of bases with a pre-weighted 5′ proximal promoter sequence constitutively bound by certain transcription factors to which additional adapter transcription factors associate on-induction via hydrophobic core interaction [33];

Non-gene intergene segments are non-transcribable promoter-less series of bases with base-associated nuclear protein hydrophobic cores, where shorter intergene segment distances constitute lesser weighted intergene distances; and

In the cases of both bullet points (2) and (3), the anionic phosphodiester moieties associate only loosely with nucleosome histone cationic lysine R-groups [45-47].

Based on these four knowns, it can be postulated with a reason degree of certainty that the necessary prerequisite for gene transcription is a cellular pressuromodulation-dependent establishment of a horizontal 5′ -> 3′ reading frame of the most asymmetrically weighted 5′ -> 3′ anisotropic intergene segment pairs with respect to the gene (wrt gene) and the lesser asymmetrically weighted 5′ -> 3′ mesotropic intergene segment pairs (wrt gene), while the symmetrically weighted 3′ -> 5′ and 5′ -> 3′ isotropic intergene segment pairs (wrt gene) remain horizontal and function as stabilizing intergene segment pairs.

Furthermore, it can be postulated with a reason degree of certainty that the conserved basis for DNA transcription and replicative gene overexpression progression to mitogenic multi-nucleation is associated with decreased cell membrane compliance primarily related to increased endocytic cell membrane pressuromodulation, which results in mitogenic multi-nucleation, for example:

In the case of the multi-nucleated giant cell [48,49] arising from the part-anchored mono-nucleated CD68+/CD163+ M2 macrophage [37,50];

In the case of the multi-nucleated (enlarged) osteoclast [51] from the part-anchored mono-nucleated TRAP+/DC-STAMP+ osteoclast [52]; and

In the case of the multi-nucleated sprouted diaphragm fenestrated lymphatic capillary endothelial cell (LEnC) [53-56] from the anchored mono-nucleated lymphatic capillary endothelial cell [53].

These cell types all proceed directly to mitogenesis multi-nucleation without preceding cell division, in the case of the multi-nucleated giant cell, due to endocytosis-episodic burst endocytosis of high-molecular-weight debris [48,49]/collagen V via episodic burst overexpression of uPARAP (Endo180; uTPAR; MRC2) [57-59]; in the case of the multi-nucleated osteoclast, due to endocytosis-episodic burst endocytosis of degraded collagen I [60,61] via episodic burst overexpression of OSCAR [51,62]; and in the case of the multi-nucleated LEnC, due to endocytosis-burst endocytosis vesiculo-vacuolo-exosomalization of cell membrane [63] via episodic burst overexpression of VEGFR2 (KDR/Flk-1) [64]. Therefore, the resultant cellular pressuromodulation of such multi-nucleated cell types is a more sustained level of greater pressuromodulation as compared with cell types that undergo mitogenesis immediately followed by cell division, which results in a significant decrease in cellular cum nuclear pressurization. As such, mitogenic without division multi-nucleated cell types can be considered model cell types to study the basis for gene overexpression in over-pressuromodulated cells as compared with the basis for gene overexpression in under-pressuromodulated non-mitogenic cells, for example, the blood microvascular capillary endothelial cell (BMEnC), which is much less pressuromodulated compared with the LEnC.

In this research study, the conserved basis for gene overexpression is studied in comparative cell types at opposing ends of pressuromodulation set point spectrum, the LEnC representing the over-pressuromodulated cell type and BMEnC representing the under-pressuromodulated cell type utilizing a published open access cDNA micro-array mRNA expression dataset [65]. The conserved basis for gene overexpression is understood in terms of the paired point tropy quotients (prpT Qs) and the 5′ -> 3′ direction episodic sub-episode block sums split-integrated weighted average-averaged gene overexpression tropy quotients (esebssiwaagoT Qs).

Methods

Data acquisition

Seven sets of most differentially overexpressed LEnC and BMEnC genes at the greater than non-adjusted twofold level and two sets of juxtaposed lesser differentially overexpressed LEnC and BMEnC genes between the non-adjusted one- to two-fold level were selected from a published open access dataset of microarray mRNA expression levels [65] (Supplementary file 1 – Supplementary Table S1). For these 18 genes, all of the transcribed loci base locations, both protein coding and noncoding, were mined utilizing the GeneCards [66] genomic neighborhood GeneLoc genome locator database [67] and the LNCipedia.org database [68].

Determination of the 3′ -> 5′ & 5′ - >3′ direction prpT Qs

Non-transcribing intergene distances were determined upstream and downstream from the gene of interest. Then, the paired point tropy quotients (prpT Q; fract) for the polymerase non-transcribing reverse 3′ -> 5′ direction (Equation 1) were determined, and the prpT Qs for the polymerase transcribing 5′ -> 3′ direction wherein the 0th order prpT Q is the first intergene distance pair prpT Q (Equation 2) were determined, as follows (Supplementary file 2 – Supplementary Table S2):

where the total number of prpT Qs is the n which achieves the n th order of 5′-> 3′ prpT Qs to either 2, 3, 4, 5 or 6 episodes.

Determination of anistropic & mesotropic sub-episode blocks for characterization of episodicity

The anisotropic and mesotropic sub-episode blocks {SEBs; anisotropic sub-episode block [ASEB], mesotropic sub-episode block [MSEB]} were determined, as follows:

Where an SEB is one with either a single, dual, triple or multiple series of prpT Qs;

Where the 0th order prpT Q SEB is the first 5′ -> 3′ prpT Q SEB;

Where an ASEB is one with one prpT Q, two prpT Qs, three prpT Qs or multiple prpT Qs of < 0.25 each;

Where the 0th order first 5′ -> 3′ prpT Q ASEB is a non-anisotropic SEB (not considered [NC]) when it is preceded by reverse anisotropy 3′ -> 5′ prpT Qs of equivalent or greater magnitude;

Where an MSEB is one with one prpT Q, two prpT Qs, three prpT Qs or multiple prpT Qs of ≥ 0.25 < 0.75 each.

An episode was then defined, as follows:

Where one episode is a single anisotropic prpT Q(s) sub-episode block (ASEB) followed by a single mesotropic prpT Q(s) sub-episode block (MSEB), or vice versa {i.e., beginning or ending with an ASEB [anisotropic period], beginning or ending with a MSEB [mesotropic period]}, with overlap between the ASEB and the MSEB periods;

Where a stabilizing isotropy (stIsotropy) intergene distance pair is an almost horizontal 5′ -> 3′ or 3′ -> 5′ intergene distance pair that has a prpT Q ≥ 0.75 (∼0 slope point) and is always considered to be the immediately preceding stabilizing intergene distance pair for an immediately proceeding SEB, either an ASEB prpT Q intergene distance pair or a MSEB prpT Q intergene distance pair;

Where instances of stIsotropy prpT Q points within an SEB are only considered after determination of the number of initial episodes for categorizing gene (either as an Episode 2, 3, 4, 5 or 6 category gene);

Where the final number of SEBs for a gene category is the number of SEBs following consideration of stIsotropy prpT Q points {5′ -> 3′ direction and 3′ -> 5′ direction [prpT Q ≥ 0.75]};

Where an immediately preceding factor-adjusted stIsotropy prpT Q point intergene distance pair (or one within an SEB) is summed with the immediately proceeding SEB prpT Q point intergene distance pair, which may result in an ASEB-to-MSEB conversion or an MSEB-to-stIsotropy conversion (i.e., of a single anisotropic prpT Q point ASEB or single mesotropic prpT Q point MSEB), and would result in an initial SEB count +/- 2 interconversion (i.e., 5 SEB -> 7 SEB; 5 SEB -> 3 SEB).

Determination of the 5′ -> 3′ direction episodic sub-episode block sums split-integrated weighted average-averaged gene overexpression tropy quotients (esebssiwaagoT Qs) to the final esebssiwaagoT Q

The complete 5′ -> 3′ direction episodic sub-episode block sums split-integrated weighted average-averaged gene overexpression tropy quotients (esebssiwaagoT Qs; fract) were determined to the final esebssiwaagoT Q in upstream anisotropic, upstream mesotropic, downstream anisotropic and downstream mesotropic parts.

First, the upstream part anisotropic sub-episode block sum (uppASEBS), the upstream part mesotropic sub-episode block sum (uppMSEBS), the downstream part ASEBS (dppASEBS) and the downstream part mesotropic sub-episode block sum (dppMSEBS) were determined.

The 5′ -> 3′ uppASEBS adjusted for uppASEBS 5′ -> 3′ stabilizing isotropy (stIsotropy) (Equation 3a), 5’ -> 3′ uppMSEBS adjusted for uppMSEBS 5′ -> 3′ stIsotropy (Equation 3b), 5′ -> 3′ dppASEBS adjusted for 5′ -> 3′ dppASEBS stIsotropy (Equation 3c), and 5′ -> 3′ dppMSEBS adjusted for dppMSEBS 5′ -> 3′ stIsotropy (Equation 3d), as follows:

Where k is an upstream 5′ -> 3′ direction intergene segment distance point in an ASEB;

Where l is an upstream 5′ -> 3′ direction intergene segment distance point in an MSEB;

Where p is a downstream 5′ -> 3′ direction intergene segment distance point in an ASEB;

Where q a downstream 5′ -> 3′ direction intergene segment distance point in an MSEB;

Where r is the upstream 5′ -> 3′ direction intergene segment distance stIsotropy point in an ASEB or in an MSEB (rn for an ASEB or MSEB with more than one stIsotropy point);

Where s is the downstream 5′ -> 3′ direction intergene segment distance stIsotropy point in an ASEB or in an MSEB (sn for an ASEB or MSEB with more than one stIsotropy point);

Where a is a1 = 0 for no preceding 5′ -> 3′ or 3′ -> 5′ stIsotropy or for preceding 5′ -> 3′ or 3′ -> 5′ stIsotropy more than (>) 5 intergene distance pairs away;

Where a is a2 = 0.125 for preceding 5′ -> 3′ or 3′ -> 5′ stIsotropy in the presence of preceding intervening 3′ -> 5′ reverse anisotropy less than or equal to (≤) 5 intergene distance pairs away;

Where a is a3 = 0.25 for immediately preceding 5′ -> 3′ or 3′ -> 5′ stIsotropy in the absence of intervening 3′ -> 5′ reverse anisotropy

The 5′ -> 3′ uppASEBS adjusted for uppASEBS 3′ -> 5′ stabilizing isotropy (stIsotropy) (Equation 3e), 5′ -> 3′ uppMSEBS adjusted for uppMSEBS 3′ -> 5′ stIsotropy (Equation 3f), 5′ -> 3′ dppASEBS adjusted for dppASEBS 3′ -> 5′ stIsotropy (Equation 3g) and the 5′ -> 3′ dppMSEBS adjusted for dppMSEBS 3′ -> 5′ stIsotropy were determined (Equation 3h), as follows:

Where t is the upstream 3′ -> 5′ direction intergene segment distance stIsotropy point in an ASEB or in an MSEB (tn for an ASEB or MSEB with more than one stIsotropy point);

Where t is also used as the downstream 3′ -> 5′ direction intergene segment distance stIsotropy point in an ASEB or in an MSEB (tn for an ASEB or MSEB with more than one stIsotropy point).

Second, the upstream part ASEB sums (uppASEBS) split-integrated weighted average (uppasebssiwa) (Equation 4a), the upstream part MSEB sums (uppMSEBS) split-integrated weighted average (uppmsebssiwa) (Equation 4b), the downstream part ASEB sums (dppASEBS) split-integrated average (dppasebssiwa) (Equation 4c), and the downstream part MSEB sums (dppMSEBS) split-integrated weighted average (dppmsebssiwa) (Equation 4d) were determined, as follows:

Where d is the number of integrated upstream part anisotropic sub-episode block sums (uppASEBS) and the number of integrated downstream part anisotropic sub-episode block sums (dppASEBS);

Where h is the number of integrated upstream part mesotropic sub-episode block sums (uppMSEBS) and the number of integrated downstream part mesotropic sub-episode block sums (dppMSEBS).

Third, the average of the uppasebssiwa and the uppmsebssiwa (uppesebssiwaa) (Equation 5a), and the average of the dppasebssiwa and the dppmsebssiwa (dppesebssiwaa) (Equation 5b) were determined, as follows:

Fourth, the complete episodic sub-episode block sums split-integrated weighted average-averaged gene overexpression tropy quotients (esebssiwaagoT Qs) (Equation 6) were determined to the final complete esebssiwaagoT Q, as follows:

Where the esebssiwaagoT Q at Episode 2 is the final esebssiwaagoT Q for genes > 11,864 ≤ 265,005 bases;

Where the esebssiwaagoT Q at Episode 3 is the final esebssiwaagoT Q for genes ≤ 11,864 bases;

Where the esebssiwaagoT Q at Episode 4 is the final esebssiwaagoT Q for genes > 265,005 < 607,463 bases;

Where the esebssiwaagoT Q at Episode 5 is the final esebssiwaagoT Q for genes ≥ 607,463 < 2,241,933 bases;

Where the esebssiwaagoT Q at Episode 6 is the final esebssiwaagoT Q for genes ≥ 2,241,933 bases.

Fifth, genes were determined to be either infra-pressuromodulated or supra-pressuromodulated, as follows:

Where a gene with an anisotropic final esebssiwaagoT Q for genes < 0.25 is a infra-pressuromodulated gene (Infra gene);

Where a gene with a mesotropic final esebssiwaagoT Q for genes ≥ 0.25 < 0.75 is a supra-pressuromodulated gene (Supra gene).

Plotting of sub-episode block sum (ASEBS, MSEBS) & final esebssiwaagoT data

The 5′ -> 3′ downstream part ASEBS (dppASEBS) (x-axis) and the 5′ -> 3′ upstream part ASEBS (uppASEBS) (y-axis) point data; the 5′ -> 3′ downstream part MSEBS (dppMSEBS) (x-axis) and the 5′ -> 3′ upstream part MSEBS (uppMSEBS) (y-axis) point data; and the final 5′ -> 3′ downstream part episodic sub-episode block sums split-integrated weighted average-average (dppesebssiwaa) (x-axis) and the final 5′ -> 3′ upstream part episodic sub-episode block sums split-integrated weighted average-average (uppesebssiwaa) (y-axis) point data were log plotted as the final complete episodic sub-episode block sums split-integrated weighted average-averaged gene overexpression tropy quotient (final esebssiwaagoT Q). In cases where there was preceding 3′ -> 5′ reverse anisotropy equivalent or greater in magnitude the reverse anisotropy points were also plotted (upstream part, x-axis; downstream part, y-axis).

Results

>11,864 ≤ 265,005 gene base category, SORL1

For SORL1, the beginning 5′ -> 3′ episodic character is dual mesotropy followed by dual anisotropy (B); the middle 5′ -> 3′ episodic character is dual mesotropy (M), stabilizing isotropy stabilized mono mesotropy followed by reverse stabilizing isotropy converted mono mesotropy-to-stabilizing isotropy and stabilized converted mono anisotropy-to-mesotropy (M); and the ending 5′ -> 3′ episodic character is multi mesotropy (E). For SORL1, the middle 3′ -> 5′ episodic character is mesotropy reverse stabilizing converting isotropy (M). SORL1 is a (5[-2]: 3) SEB Episode 2 gene (Table 1).

 

Episodic and sub-episodic block character as per the paired point tropy quotients (

Gene symbol	Number of episodes (number of final SEBs)	Beginning (B), middle (M) and ending (E) of episodic character as per 5′ -> 3′ prpTQs (SEB character)	Episodic character as per 3′ -> 5′ prpTQs	Gene type
SORL1	2(5 [-2]: 3)	(1) Dual mesotropy (B)(2) Dual anisotropy deviation from constancy variant (B)(3a) Dual mesotropy (M)(3b) Stabilizing isotropy stabilized mono mesotropy (M)(3c) Reverse stabilizing isotropy converted mono mesotropy-to-stabilizing isotropy and stabilized converted mono anisotropy-to-mesotropy (M)(3d) Multi mesotropy (E)	Mesotropy reverse stabilizing converting isotropy (M)	Supra
PDPN	2(5)	(1a) Reverse stabilizing isotropy converted mono mesotropy-to-stabilizing isotropy and stabilized mono mesotropy (B)(1b) Mono mesotropy (B)(2) Mono anisotropy (B)(3a) Tri mesotropy (M)(3b) Stabilizing isotropy and reverse stabilizing isotropy stabilized mono mesotropy (M)(3c) Stabilizing isotropy stabilized mono mesotropy (M)(4) Mono anisotropy (M)(5)Reverse stabilizing isotropy stabilized mono mesotropy (E)	Mesotropy reverse stabilizing converting isotropy (B)Mesotropy reverse stabilizing isotropy (M)Mesotropy reverse stabilizing isotropy (E)	Supra
BTG1	2(5)	(1) Tri anisotropy (B)(2a) Tri mesotropy (B)(2b) Reverse stabilizing isotropy stabilized mono mesotropy (B)(2c) Mono mesotropy (B)(NC 3a) non-mono anisotropy (M)(3b) Stabilizing isotropy stabilized mono anisotropy (M)(3c) Mono anisotropy (M)(4) Mono mesotropy (M)(5a) Reverse stabilizing isotropy stabilized mono anisotropy (E)(5b) Dual anisotropy (E)	Mesotropy reverse stabilizing isotropy (B)Reverse anisotropy (M),Anisotropy reverse stabilizing isotropy (E)	Supra
HAPLN1	2(5 [+2]: 7)	(1) Dual mesotropy (B)(2) Mono anisotropy (B)(3) Stabilizing isotropy converted mono anisotropy-to-mesotropy (B)(4) Stabilizing isotropy stabilized mono anisotropy (B)(5a) Mono mesotropy (M)(5b) Reverse stabilizing isotropy stabilized mono mesotropy (M)(5c) Mono mesotropy (M)(6) Mono anisotropy (M)(7) Mono mesotropy (E)	Mesotropy reverse stabilizing isotropy (M)	Supra
MRC1	2(5 [+2]: 7)	(1) Multi (6) anisotropy (B)(2) Stabilizing isotropy and reverse stabilizing isotropy converted mono anisotropy-to-mesotropy (B)(3) Mono anisotropy (B)(4a) Stabilizing isotropy stabilized mono mesotropy (B)(4b) Stabilizing isotropy stabilized mono mesotropy (B)(5) Dual anisotropy (M)(6) Dual mesotropy (M)(7) Multi (4) anisotropy (E)	Anisotropy reverse stabilizing converting isotropy (B)	Supra
ACPP	2(5 [-2]: 3)	(NC) Nonmono anisotropy (B)(1) Mono mesotropy deviation from constancy (B)(2) Mono anisotropy (B)(3a) Mono mesotropy deviation from constancy (M)(3b) Stabilizing isotropy and reverse stabilizing isotropy converted mono anisotropy-to-mesotropy deviation from constancy (M)(3c) Mono mesotropy deviation from constancy (E)	Reverse anisotropy (B)	Supra
TGFA	2(5)	(1a) Stabilizing isotropy stabilized mono mesotropy (B)(1b) Dual mesotropy (B)(2a) Mono anisotropy (B)(2b) Reverse stabilizing isotropy stabilized mono anisotropy (B)(2c) Mono anisotropy (B)(3a) Mono mesotropy (M)(3b) Reverse stabilizing isotropy stabilized mono mesotropy (M)(3c) Stabilizing isotropy and reverse stabilizing isotropy converted mono anisotropy-to-mesotropy (M)(4) Mono anisotropy (M)(5) Tri mesotropy (E)	Anisotropy reverse stabilizing isotropy (B)Mesotropy reverse stabilizing isotropy (M)Anisotropy reverse stabilizing converting isotropy (M)	Supra
PHLPP1	2(5)	(1) Tri mesotropy (B)(2) Mono anisotropy (B) (3) Stabilizing isotropy and reverse stabilizing isotropy converted mono mesotropy-to stabilizing isotropy and stabilized mono mesotropy (M)(4a) Stabilizing isotropy stabilized mono anisotropy (M)(4b) Mono anisotropy (M)(5) Mono mesotropy (E)	Mesotropy reverse stabilizing converting isotropy (M)	Supra
SELE	2(5 [+2]: 7)	(1) Stabilizing isotropy stabilized mono anisotropy (B)(2) Dual mesotropy (B)(3a) Mono anisotropy (M)(3b) Stabilizing isotropy stabilized mono anisotropy (M)(3c) Mono anisotropy (M)(4) Reverse stabilizing isotropy converted anisotropy-to-mesotropy (M)(5) Dual anisotropy (M)(6) Mono mesotropy (M)(7a) Stabilizing isotropy stabilized mono anisotropy (E)(7b) Mono anisotropy (E)	Anisotropy reverse stabilizing isotropy (M)Anisotropy reverse converting stabilizing isotropy (M)	Infra
CDH11	2(5)	(1) Mono mesotropy (B)(2) Reverse stabilizing isotropy stabilized mono anisotropy (B)(3) Mono mesotropy (M)(4) Dual anisotropy (M)(5) Dual mesotropy (E)	Anisotropy reverse stabilizing isotropy (M)	Infra
ZCCHC2 (C18orf49;KIAA1744)	2(5 [+2]: 7)	(1) Mono anisotropy (B)(2) Reverse stabilizing isotropy converted anisotropy-to-mesotropy (B)(3) Mono anisotropy (B)(4a) Dual stabilizing isotropy converted anisotropy-to-mesotropy (B)(4b) Stabilizing isotropy stabilized mono mesotropy (B)(5) Mono anisotropy (M)(6) Dual mesotropy (M)(7) Multi (5) anisotropy (E)	Anisotropy reverse stabilizing converting isotropy (B)	Infra
S100A2	3(7)	(1) Reverse stabilizing isotropy stabilized mono anisotropy (B)(2) Dual mesotropy (B)(3) Mono anisotropy (M)(4) Reverse stabilizing isotropy stabilized mono mesotropy (M)(5) Multi anisotropy (M)(6a) Mono mesotropy (M)(6b) Stabilizing isotropy and reverse stabilizing isotropy stabilized mono mesotropy (M)(7) Stabilizing isotropy stabilized mono anisotropy (E)	Anisotropy reverse stabilizing isotropy (B)Mesotropy reverse stabilizing isotropy (M)Mesotropy reverse stabilizing Isotropy (M)	Supra
PRR3	3(7 [+2]: 9)	(1a) Stabilizing isotropy stabilized mono anisotropy (B)(1b) Mono anisotropy (B)(2) Dual mesotropy (B)(3) Mono anisotropy (M)(4) Reverse stabilizing isotropy converted anisotropy-to-mesotropy (M)(5) Dual anisotropy (M)(6a) Stabilizing isotropy stabilized mono mesotropy (M)(6b) Dual mesotropy (M)(7) Multi (6) anisotropy (M)(8) Multi mesotropy (M)(9) Multi (6) anisotropy (E)	Anisotropy reverse stabilizing isotropy (M)	Infra
IFI27	3(7)	(1) Mono anisotropy (B)(2) Mono mesotropy (B)(3) Dual anisotropy (M)(4) Tri mesotropy (M)(5a) Dual anisotropy (M)(5b) Stabilizing isotropy stabilized mono anisotropy (M)(5c) Dual anisotropy (M)(6) Stabilizing isotropy and reverse stabilizing isotropy stabilized mono mesotropy (M)(7) Mono anisotropy (E)	Mesotropy reverse stabilizing isotropy (B)	Infra
S100A14	3(7)	(1a) Tri mesotropy (B)(1b) Stabilizing isotropy stabilized mono mesotropy (B)(1c) Stabilizing isotropy stabilized mono mesotropy (B)(1d) Stabilizing isotropy converted mono anisotropy-to-mesotropy (B)(2) Mono anisotropy (B)(3) Dual mesotropy (M)(4a) Stabilizing isotropy stabilized mono anisotropy (M)(4b) Mono anisotropy (M)(5a) Dual stabilizing isotropy and dual reverse stabilizing isotropy stabilized mono mesotropy (M)(5b) Mono mesotropy (M)(6) Multi anisotropy (M)(7) Stabilizing isotropy stabilized mono mesotropy (E)	Mesotropy reverse stabilizing isotropy (M)Mesotropy reverse stabilizing isotropy (M)	Infra
ABCB1	4(9 [-2]: 7)	(1) Stabilizing isotropy stabilized, reverse stabilizing isotropy stabilized, reverse stabilizing isotropy stabilized and stabilizing isotropy stabilized mono mesotropy (B)(2) Tri anisotropy (B)(3) Dual mesotropy (M)(4) Mono anisotropy (M)(5) Mono mesotropy (M)(6) Tri anisotropy (M)(7a) Mono mesotropy (M)(7b) Stabilizing isotropy and reverse stabilizing isotropy stabilized mono mesotropy (M)(7c) Stabilizing isotropy converted anisotropy-to-mesotropy (E)(7d) Dual mesotropy (E)	Mesotropy reverse stabilizing isotropy (B)Mesotropy reverse stabilizing isotropy (B)Mesotropy reverse stabilizing isotropy (M)	Infra
FOXP2	5(11)	(1) Reverse stabilizing isotropy converted mono mesotropy-to-stabilizing isotropy and stabilized mono mesotropy (B)(2) Mono anisotropy (B)(3) Tri mesotropy (M)(4) Multi (4) anisotropy (M)(5) Dual mesotropy (M)(6) Mono anisotropy (M)(7a) Stabilizing isotropy stabilized mono mesotropy (M)(7b) Mono mesotropy (M)(8) Mono anisotropy (M)(9) Dual mesotropy (M)(10) Tri anisotropy (M)(11) Mono mesotropy (E)	Mesotropy reverse stabilizing converting isotropy (B)	Infra
DMD	6(13)	(1) Mono anisotropy (B)(2a) Mono mesotropy (B)(2b) Stabilizing isotropy and part-reverse stabilizing isotropy stabilized mono mesotropy (B)(3) Tri anisotropy (M)(4a) Stabilizing isotropy stabilized mono mesotropy (M)(4b) Mono mesotropy (M)(5) Dual anisotropy (M)(6) Mono mesotropy (M)(7a) Stabilizing isotropy stabilized mono anisotropy (M)(7b) Multi (6) anisotropy (M)(8) Mono mesotropy (M)(9) Mono anisotropy (M)(10) Mono mesotropy (M)(11) Mono anisotropy (M)(12) Mono mesotropy (M)(13) Mono anisotropy (E)	(TC) Mesotropy part-reverse stabilizing isotropy (B)Reverse anisotropy (B)Reverse anisotropy (B)	Infra

For SORL1, there are two final MSEBs and there is one final ASEB (Figure 1). For SORL1, the integrated uppmsebssiwa is 65,960 at Episode 2 (h = 2) and the integrated uppasebssiwa is 33,201 at Episode 2 (d = 1); and the integrated dppmsebssiwa is 144,058 at Episode 2 (h = 2) and the integrated dppasebssiwa is 203,780 at Episode 2 (d = 1). For SORL1, the uppesebssiwaa is 49,581 and the dppesebssiwaa is 173,919 that results in an esebssiwaagoT Q of 0.29 at Episode 2. SORL1 meets the threshold of ≥ 0.25 < 0.75 for a supra-pressuromodulated gene (Table 2 & Supplementary file 3 – Supplementary Table S3).

 

>11,864 ≤265,005 gene base category,

 

Final episodic sub-episode block sums split-integrated weighted average-averaged gene overexpression tropy quotient (

Gene symbol	Number of transcribed gene bases	Gene base category	Uppasebssiwa + uppmsebssiwa2	Dppasebssiwa + dppmsebssiwa2	uppesebssiwaadppesebssiwaa	esebssiwaagoTQ	Gene type
SORL1	181,560(197,782)	>11,864≤ 265,005	33,201 + 65,9602	203,780 + 144,0582	49,581173,919	0.29(@ Episode 2)	Supra
PDPN	34,493	> 11,864≤ 265,005	2867 + 25,8752	24,905 + 45,6972	14,37135,301	0.41(@ Episode 2)	Supra
BTG1	5620(160,922)	>11,864≤265,005	23,241 + 84,9392	235,679 + 188,8942	54,090212,287	0.25(@ Episode 2)	Supra
HAPLN1	83,809	>11,864≤265,005	11,635 + 71,2282	90,544 + 144,0302	41,431117,287	0.35(@ Episode 2)	Supra
MRC1	101,828	>11,864≤265,005	29,632 + 50,3932	198,095 + 91,1362	46,390148,945	0.28(@ Episode 2)	Supra
ACPP	50,936	>11,864≤265,005	3600 + 34,4382	56,613 + 96,7212	19,01976,667	0.25(@ Episode 2)	Supra
TGFA	106,914	>11,864≤265,005	9528 + 53,1142	84,199 + 124,6632	24,92981,129	0.31(@ Episode 2)	Supra
PHLPP1	265,005	>11,864≤265,005	10,343 + 49,4762	80,268 + 92,6872	29,91086,477	0.35(@ Episode 2)	Supra
SELE	42,066(74,076)	>11,864≤265,005	8849 + 32,1292	120,813 + 84,4042	20,489102,609	0.20(@ Episode 2)	Infra
CDH11	182,360	>11,864≤265,005	8781 + 42,6442	333,604 + 84,2682	25,713208,936	0.12(@ Episode 2)	Infra
ZCCHC2	64,703	>11,864≤265,005	25,000 + 34,5912	246,271 + 97,5242	29,796171,898	0.17(@ Episode 2)	Infra
S100A2	6783	≤11,864	3916 + 17,7592	40,214 + 29,2982	10,83834,756	0.31(@ Episode 3)	Supra
PRR3	7988	≤11,864	5063 + 14,1142	53,078 + 27,5852	958840,331	0.24(@ Episode 3)	Infra
IFI27	11,864	≤11,864	18,359 + 42,0102	151,833 + 108,0532	30,185129,943	0.23(@ Episode 3)	Infra
S100A14	2732(4051)	≤11,864	8033 + 21,5232	188,934 + 53,2042	14,778121,069	0.12(@ Episode 3)	Infra
ABCB1	209,691(386,184)	>265,005<607,463	18,256 + 74,1632	355,477 + 161,9252	46,210258,701	0.18(@ Episode 4)	Infra
FOXP2	607,463	≥607,463<2,241,933	15,948 + 69,5832	273,470 + 140,5832	42,754207,027	0.21(@ Episode 5)	Infra
DMD	2,241,933	≥2,241,933	32,973 + 74,2922	296,028 + 163,5702	53,632229,799	0.23(@ Episode 6)	Infra

>11,864 ≤265,005 gene base category, PDPN

For PDPN, the beginning 5′ -> 3′ episodic character is reverse stabilizing isotropy converted mono mesotropy-to-stabilizing isotropy and stabilized mono mesotropy (B), mono mesotropy (B) followed by mono anisotropy (B); the middle 5′ -> 3′ episodic character is tri mesotropy (M), stabilizing isotropy and reverse stabilizing isotropy stabilized mono mesotropy (M), stabilizing isotropy stabilized mono mesotropy (M) followed by mono anisotropy (M); and the ending 5′ -> 3′ episodic character is reverse stabilizing isotropy stabilized mono mesotropy (E). For PDPN, the beginning 3′ -> 5′ episodic character is mesotropy reverse stabilizing converting isotropy (B); the middle 3′ -> 5′ episodic character is mesotropy reverse stabilizing isotropy (M); and the ending 3′ -> 5′ episodic character is mesotropy reverse stabilizing isotropy (E). PDPN is a (5) SEB Episode 2 gene (Table 1).

For PDPN, there are three final MSEBs and there are two final ASEBs (Figure 2). For PDPN, the integrated uppmsebssiwa is 25,875 at Episode 2 (h = 3) and the integrated uppasebssiwa at Episode 2 is 2867 (d = 2); and the integrated dppmsebssiwa is 45,697 at Episode 2 (h = 3) and the integrated dppasebssiwa is 24,905 at Episode 2 (d = 2). For PDPN, the uppesebssiwaa is 14,371 and the dppesebssiwaa is 35,301 that results in an esebssiwaagoT Q of 0.41 at Episode 2. PDPN meets the threshold of ≥ 0.25 < 0.75 for a supra-pressuromodulated gene (Table 2 & Supplementary file 3 – Supplementary Table S3).

 

>11,864 ≤265,005 gene base category,

>11,864 ≤265,005 gene base category, BTG1

For BTG1, the beginning 5′ -> 3′ episodic character is tri anisotropy (B), tri mesotropy (B), reverse stabilizing isotropy stabilized mono mesotropy (B) followed by mono mesotropy (B); the middle 5′ -> 3′ episodic character is not considered (NC) non-mono anisotropy (M), stabilizing isotropy stabilized mono anisotropy (M), mono anisotropy (M) followed by mono mesotropy (M); and the ending 5′ -> 3′ episodic character is reverse stabilizing isotropy stabilized mono anisotropy (E) followed by dual anisotropy (E). For BTG1, the beginning 3′ -> 5′ episodic character is mesotropy reverse stabilizing isotropy (B), the middle 3′ -> 5′ episodic character is reverse anisotropy (M); and the ending 3′ -> 5′ episodic character is anisotropy reverse stabilizing isotropy (E). BTG1 is a (5) SEB Episode 2 gene (Table 1).

For BTG1, there are two final MSEBs (first MSEBS 259,332, 131,445; second MSEBS 118,464, 42,123), and there are three final ASEBs (first ASEBS 120,346, 5,971; second ASEBS 419,487, 57,054; third ASEBS 171,058, 6,711). There is the first non-mono anisotropic point (95,217, 4,153) of the second ASEBS (419,487, 57,054) that is not considered (NC) as there is an immediately preceding 3′ -> 5′ reverse anisotropic point of equivalent magnitude (79, 93,667) (Figure 3). For BTG1, the integrated uppmsebssiwa is 84,939 at Episode 2 (h = 2) and the integrated uppasebssiwa at Episode 2 is 23,241 (d = 3); and the integrated dppmsebssiwa at Episode 2 is 188,894 (h = 2) and the integrated dppasebssiwa at Episode 2 is 235,679 (d = 3). For BTG1, the uppesebssiwaa is 54,090 and the dppesebssiwaa is 212,287 that results in an esebssiwaagoT Q of 0.25 at Episode 2. BTG1 meets the threshold of ≥ 0.25 < 0.75 for a supra-pressuromodulated gene (Table 2 & Supplementary file 3 – Supplementary Table S3).

 

>11,864 ≤265,005 gene base category,

Filled green square, first non-mono anisotropic point (95,217, 4,153) of the second ASEBS (419,487, 57,054) shown without the non-mono anisotropic point (95,217, 4,153); green star, immediately preceding 3′ -> 5′ reverse anisotropic point 78, 93,666.

> 11,864 ≤ 265,005 gene base category, HAPLN1

For HAPLN1, the beginning 5′ -> 3′ episodic character is dual mesotropy (B), mono anisotropy (B), stabilizing isotropy converted mono anisotropy-to-mesotropy (B) followed by stabilizing isotropy stabilized mono anisotropy (B); the middle 5′ -> 3′ episodic character is mono mesotropy (M), reverse stabilizing isotropy stabilized mono mesotropy (M), mono mesotropy (M) followed by mono anisotropy (M); and the ending 5′ -> 3′ episodic character is mono mesotropy (E). For HALPN1, the middle 3′ -> 5′ episodic character is mesotropy reverse stabilizing isotropy (M). HAPLN1 is a [5(+2): 7] SEB Episode 2 gene (Table 1).

For HAPLN1, there are four final MSEBs and there are three final ASEBs (Figure 4). For HAPLN1, the integrated uppmsebssiwa is 71,228 at Episode 2 (h = 4) and the integrated uppasebssiwa is 11,635 at Episode 2 (d = 3); and the integrated dppmsebssiwa is 144,030 at Episode 2 (h = 4) and the integrated dppasebssiwa is 90,544 at Episode 2 (d = 3). For HAPLN1, the uppesebssiwaa is 41,431 and the dppesebssiwaa is 117,287 that results in an esebssiwaagoT Q of 0.35 at Episode 2. HAPLN1 meets the threshold of ≥ 0.25 < 0.75 for a supra-pressuromodulated gene (Table 2 & Supplementary file 3 – Supplementary Table S3).

 

>11,864 ≤265,005 gene base category,

>11,864 ≤265,005 gene base category, MRC1

For MRC1, the beginning 5′ -> 3′ episodic character is multi (6) anisotropy [B], stabilizing isotropy and reverse stabilizing isotropy converted mono anisotropy-to-mesotropy (B), mono anisotropy (B), stabilizing isotropy stabilized mono mesotropy (B) followed by stabilizing isotropy stabilized mono mesotropy (B); the middle 5′ -> 3′ episodic character is dual anisotropy (M) followed by dual mesotropy (M); and the ending 5′ -> 3′ episodic character is multi (4) anisotropy (E). For MRC1, the beginning 3′ -> 5′ episodic character is anisotropy reverse stabilizing converting isotropy (B). MRC1 is a (5 [+2]: 7) SEB Episode 2 gene (Table 1).

For MRC1, there are 3 final MSEBs and there are 4 final ASEBs (Figure 5). For MRC1, the integrated uppmsebssiwa is 50,393 at Episode 2 (h = 3) and the integrated uppasebssiwa is 29,632 at Episode 2 (d = 4); and the integrated dppmsebssiwa is 91,136 at Episode 2 (h = 3) and the integrated dppasebssiwa is 198,095 at Episode 2 (d = 4). For MRC1, the uppesebssiwaa is 46,390 and the dppesebssiwaa is 148,945 that results in an esebssiwaagoT Q of 0.28 at Episode 2. MRC1 meets the threshold of ≥ 0.25 < 0.75 for a supra-pressuromodulated gene (Table 2 & Supplementary file 3 – Supplementary Table S3).

 

>11,864 ≤265,005 gene base category,

>11,864 ≤265,005 gene base category, ACPP

For ACPP, the beginning 5′ -> 3′ episodic character is NC nonmono anisotropy (B), mono mesotropy deviation from constancy (B) followed by mono anisotropy (B); the middle 5′ -> 3′ episodic character is mono mesotropy deviation from constancy (M) followed by stabilizing isotropy and reverse stabilizing isotropy converted mono anisotropy-to-mesotropy deviation from constancy (M); and the ending 5′ -> 3′ episodic character is mono mesotropy deviation from constancy (E). For ACPP, the beginning 3′ -> 5′ episodic character is reverse anisotropy (B). ACPP is a (5 [-2]: 3) SEB Episode 2 gene (Table 1).

For ACPP, of the considered SEBs, there are two final MSEBs (first MSEBS 26,298, 10,139; second MSEBS 167,150, 58,743), and there is one final mono-ASEB (first and only ASEBS 56,614, 3601). The non-mono-anisotropic not considered (NC) SEB (NC ASEBS 26,865, 1099) is the 0 order SEB as there are a series of six preceding 3′ -> 5′ reverse anisotropic points of greater magnitude (Figure 6). For ACPP, the integrated uppmsebssiwa is 34,438 at Episode 2 (h = 2) and the integrated uppasebssiwa is 3600 at Episode 2 (d = 1); and the integrated dppmsebssiwa is 96,721 at Episode 2 (h = 2) and the integrated dppasebssiwa is 56,613 at Episode 2 (d = 1). For ACPP, the uppesebssiwaa is 19,019 and the dppesebssiwaa is 76,667 that results in an esebssiwaagoT Q of 0.25 at Episode 2. ACPP meets the threshold of ≥ 0.25 < 0.75 for a supra-pressuromodulated gene (Table 2 & Supplementary file 3 – Supplementary Table S3).

 

>11,864 ≤265,005 gene base category,

Filled green square, non-mono anisotropic not considered (NC) first sub-episode block (SEB) (NC ASEBS 26,865, 1,099) due to six preceding 3′-> 5′ reverse anisotropic points of greater magnitude (Green stars), in which case the 0 order prpT Q SEB (first considered SEB) is the immediately following SEB, a mesotropic SEB.

>11,864 ≤265,005 gene base category, TGFA

For TGFA, the beginning 5′ -> 3′ episodic character is stabilizing isotropy stabilized mono mesotropy (B), dual mesotropy (B), mono anisotropy (B), reverse stabilizing isotropy stabilized mono anisotropy (B) followed by mono anisotropy (B); the middle 5′ -> 3′ episodic character is mono mesotropy (M), reverse stabilizing isotropy stabilized mono mesotropy (M), stabilizing isotropy and reverse stabilizing isotropy converted mono anisotropy-to-mesotropy (M) followed by mono anisotropy (M); and the ending 5′ -> 3′ episodic character is tri mesotropy (E). For TGFA, the beginning 3′ -> 5′ episodic character is anisotropy reverse stabilizing isotropy (B); and the middle 3′ -> 5′ episodic character is mesotropy reverse stabilizing isotropy (M) and anisotropy reverse stabilizing converting isotropy (M). TGFA is a (5) SEB Episode 2 gene (Table 1).

For TGFA, there are three final MSEBs and there are two final ASEBs (Figure 7). For TGFA, the integrated uppmsebssiwa is 53,114 at Episode 2 (h = 3) and the integrated uppasebssiwa is 9528 at Episode 2 (d = 2); and the integrated dppmsebssiwa is 124,663 at Episode 2 (h = 3) and the integrated dppasebssiwa is 84,199 at Episode 2 (d = 2). For TGFA, the uppesebssiwaa is 24,929 and the dppesebssiwaa is 81,129 that results in an esebssiwaagoT Q of 0.31 at Episode 2. TGFA meets the threshold of ≥ 0.25 < 0.75 for a supra-pressuromodulated gene (Table 2 & Supplementary file 3 – Supplementary Table S3).

 

>11,864 ≤265,005 gene base category,

>11,864 ≤265,005 gene base category, PHLPP1

For PHLPP1, the beginning 5′ -> 3′ episodic character is tri mesotropy (B) followed by mono anisotropy (B); the middle 5′ -> 3′ episodic character is stabilizing isotropy and reverse stabilizing isotropy converted mono mesotropy-to stabilizing isotropy and stabilized mono mesotropy (M), stabilizing isotropy stabilized mono anisotropy (M), mono anisotropy (M), mono mesotropy (M) followed by mono anisotropy (M); and the ending 5′ -> 3′ episodic character is dual mesotropy (E). For PHLPP1, the middle 3′ -> 5′ episodic character is mesotropy reverse stabilizing converting isotropy (M). PHLPP1 is a (5) SEB Episode 2 gene (Table 1).

For PHLPP1, there are three final MSEBs and there are two final ASEBs (Figure 8). For PHLPP1, the integrated uppmsebssiwa is 49,476 at Episode 2 (h = 3) and the integrated uppasebssiwa is 10,343 at Episode 2 (d = 2); and the integrated dppmsebssiwa is 92,687 at Episode 2 (h = 3) and the integrated dppasebssiwa is 80,268 at Episode 2 (d = 2). For PHLPP1, the uppesebssiwaa is 29,910 and the dppesebssiwaa is 86,477 that results in an esebssiwaagoT Q of 0.35 at Episode 2. PHLPP1 meets the threshold of ≥ 0.25 < 0.75 for a supra-pressuromodulated gene (Table 2 & Supplementary file 3 – Supplementary Table S3).

 

>11,864 ≤265,005 gene base category,

>11,864 ≤265,005 gene base category, SELE

For SELE, the beginning 5′ -> 3′ episodic character is stabilizing isotropy stabilized mono anisotropy (B) followed dual mesotropy (B); the middle 5′ -> 3′ episodic character is mono anisotropy (M), stabilizing isotropy stabilized mono anisotropy (M), mono anisotropy (M), reverse stabilizing isotropy converted anisotropy-to-mesotropy (M), dual anisotropy (M) followed by mono mesotropy (M); and the ending 5′ -> 3′ episodic character is stabilizing isotropy stabilized mono anisotropy (E) followed by mono anisotropy (E). For SELE, the middle 3′ -> 5′ episodic character is anisotropy reverse stabilizing isotropy (M) and anisotropy reverse converting stabilizing isotropy (M). SELE is a [5(+2): 7] SEB Episode 2 gene (Table 1).

For SELE, there are three final MSEBs and there are four final ASEBs (Figure 9). For SELE, the integrated uppmsebssiwa is 32,129 at Episode 2 (h = 3) and the integrated uppasebssiwa is 8,849 at Episode 2 (d = 4); and the integrated dppmsebssiwa is 84,404 at Episode 2 (h = 3) and the integrated dppasebssiwa is 120,813 at Episode 2 (d = 4). For SELE, the uppesebssiwaa is 20,489 and the dppesebssiwaa is 102,609 that results in an esebssiwaagoT Q of 0.20 at Episode 2. SELE meets the threshold of < 0.25 for an infra-pressuromodulated gene (Table 2 & Supplementary file 3 – Supplementary Table S3).

 

>11,864 ≤265,005 gene base category,

>11,864 ≤265,005 gene base category, CDH11

For CDH11, the beginning 5′ -> 3′ episodic character is mono mesotropy (B) followed by reverse stabilizing isotropy stabilized mono anisotropy (B); the middle 5′ -> 3′ episodic character is mono mesotropy (M) followed by dual anisotropy (M); and the ending 5′ -> 3′ episodic character is dual mesotropy (E). For CDH11, the middle 3′ -> 5′ episodic character is anisotropy reverse stabilizing isotropy (M). CDH11 is a (5) SEB Episode 2 gene (Table 1).

For CDH11, there are three final MSEBs and there are two final ASEBs (Figure 10). For CDH11, the integrated uppmsebssiwa is 42,644 at Episode 2 (h = 3) and the integrated uppasebssiwa is 8781 at Episode 2 (d = 2); and the integrated dppmsebssiwa is 84,268 at Episode 2 (h = 3) and the integrated dppasebssiwa is 333,604 at Episode 2 (d = 2). For CDH11, the uppesebssiwaa is 25,713 and the dppesebssiwaa is 208,936 that results in an esebssiwaagoT Q of 0.12 at Episode 2. CDH11 meets the threshold of < 0.25 for an infra-pressuromodulated gene (Table 2 & Supplementary file 3 – Supplementary Table S3).

 

>11,864 ≤265,005 gene base category,

>11,864 ≤265,005 gene base category, ZCCHC2

For ZCCHC2, the beginning 5′ -> 3′ episodic character is mono anisotropy (B), reverse stabilizing isotropy converted anisotropy-to-mesotropy (B), mono anisotropy (B), dual stabilizing isotropy converted anisotropy-to-mesotropy (B) followed by stabilizing isotropy stabilized mono mesotropy (B); the middle 5′ -> 3′ episodic character is mono anisotropy (M) followed by dual mesotropy (M); and the ending 5′ -> 3′ episodic character is multi (5) anisotropy (E). For ZCCHC2, the beginning 3′ -> 5′ episodic character is anisotropy reverse stabilizing converting isotropy (B). ZCCHC2 is a (5 [+2]: 7) SEB Episode 2 gene (Table 1).

For ZCCHC2, there are three final MSEBs and there are four final ASEBs (Figure 11). For ZCCHC2, the integrated uppmsebssiwa is 34,591 at Episode 2 (h = 3) and the integrated uppasebssiwa is 25,000 at Episode 2 (d = 4); and the integrated dppmsebssiwa is 97,524 at Episode 2 (h = 3) and the integrated dppasebssiwa is 246,271 at Episode 2 (d = 4). For ZCCHC2, the uppesebssiwaa is 29,796 and the dppesebssiwaa is 171,898 that results in an esebssiwaagoT Q of 0.17 at Episode 2. ZCCHC2 meets the threshold of < 0.25 for an infra-pressuromodulated gene (Table 2 & Supplementary file 3 – Supplementary Table S3).

 

>11,864 ≤265,005 gene base category,

≤ 11,864 gene base category, S100A2

For S100A2, the beginning 5′ -> 3′ episodic character is reverse stabilizing isotropy stabilized mono anisotropy (B) followed by dual mesotropy (B); the middle 5′ -> 3′ episodic character is mono anisotropy (M), reverse stabilizing isotropy stabilized mono mesotropy (M), multi anisotropy (M), mono mesotropy (M) followed by stabilizing isotropy and reverse stabilizing isotropy stabilized mono mesotropy (M); and the ending 5′ -> 3′ episodic character is stabilizing isotropy stabilized mono anisotropy (E). For S100A2, the beginning 3′ -> 5′ episodic character is anisotropy reverse stabilizing isotropy (B); and the middle 3′ -> 5′ episodic character is mesotropy reverse stabilizing isotropy (M) and mesotropy reverse stabilizing isotropy (M). S100A2 is a (7) SEB Episode 3 gene (Table 1).

For S100A2, there are three final MSEBs and there are four final ASEBs (Figure 12). For S100A2, the integrated uppmsebssiwa is 17,298 at Episode 3 (h = 3) and the integrated uppasebssiwa is 3916 at Episode 3 (d = 4); and the integrated dppmsebssiwa is 29,298 at Episode 3 (h = 3) and the integrated dppasebssiwa is 40,214 at Episode 3 (d = 4). For S100A2, the uppesebssiwaa is 10,838 and the dppesebssiwaa is 34,756 that results in an esebssiwaagoT Q of 0.31 at Episode 3. S100A2 meets the threshold of ≥ 0.25 < 0.75 for a supra-pressuromodulated gene (Table 2 Supplementary file 3 – Supplementary Table S3).

 

≤11,864 gene base category,

≤11,864 gene base category, PRR3

For PRR3, the beginning 5′ -> 3′ episodic character is stabilizing isotropy stabilized mono anisotropy (B), mono anisotropy (B) followed by dual mesotropy (B); the middle 5′ -> 3′ episodic character is mono anisotropy (M), reverse stabilizing isotropy converted anisotropy-to-mesotropy (M), dual anisotropy (M), stabilizing isotropy stabilized mono mesotropy (M), dual mesotropy (M), multi (6) anisotropy (M) followed by multi mesotropy (M); and the ending 5′ -> 3′ episodic character is multi (6) anisotropy (E). For PRR3, the middle 3′ -> 5′ episodic character is anisotropy reverse stabilizing isotropy (M). PRR3 is a [7(+2): 9] SEB Episode 3 gene (Table 1).

For PRR3, there are four final MSEBs and there are five final ASEBs (Figure 13). For PRR3, the integrated uppmsebssiwa is 14,114 at Episode 3 (h = 4) and the integrated uppasebssiwa is 5063 at Episode 3 (d = 5); and the integrated dppmsebssiwa is 27,585 at Episode 3 (h = 4) and the integrated dppasebssiwa is 53,078 at Episode 3 (d = 5). For PRR3, the uppesebssiwaa is 9588 and the dppesebssiwaa is 40,331 that results in an esebssiwaagoT Q of 0.24 at Episode 3. PRR3 meets the threshold of < 0.25 for an infra-pressuromodulated gene (Table 2 & Supplementary file 3 – Supplementary Table S3).

 

≤11,864 gene base category,

≤11,864 gene base category, IFI27

For IFI27, the beginning 5′ -> 3′ episodic character is mono anisotropy (B) followed by mono mesotropy (B); the middle 5′ -> 3′ episodic character is dual anisotropy (M), tri mesotropy (M), dual anisotropy (M), stabilizing isotropy stabilized mono anisotropy (M), dual anisotropy (M) followed by stabilizing isotropy and reverse stabilizing isotropy stabilized mono mesotropy (M); and the ending 5′ -> 3′ episodic character is mono anisotropy (E). For IFI27, the beginning 3′ -> 5′ episodic character is mesotropy reverse stabilizing isotropy (B). IFI27 is a (7) SEB Episode 3 gene (Table 1).

For IFI27, there are three final MSEBs and there are 4 final ASEBs (Figure 14). For IFI27, the integrated uppmsebssiwa is 42,010 at Episode 3 (h = 3) and the integrated uppasebssiwa is 18,359 at Episode 3 (d = 4); and the integrated dppmsebssiwa is 108,053 at Episode 3 (h = 3) and the integrated dppasebssiwa is 151,833 at Episode 3 (d = 4). For IFI27, the uppesebssiwaa is 30,185 and the dppesebssiwaa is 129,943 that results in an esebssiwaagoT Q of 0.23 at Episode 3. IFI27 meets the threshold of < 0.25 for an infra-pressuromodulated gene (Table 2 & Supplementary file 3 – Supplementary Table S3).

 

≤11,864 gene base category,

≤11,864 gene base category, S100A14

For S100A14, the beginning 5′ -> 3′ episodic character is tri mesotropy (B), stabilizing isotropy stabilized mono mesotropy (B), stabilizing isotropy stabilized mono mesotropy (B), stabilizing isotropy converted mono anisotropy-to-mesotropy (B) followed by mono anisotropy (B); the middle 5′ -> 3′ episodic character is dual mesotropy (M), stabilizing isotropy stabilized mono anisotropy (M), mono anisotropy (M), dual stabilizing isotropy and dual reverse stabilizing isotropy stabilized mono mesotropy (M), mono mesotropy (M) followed by multi anisotropy (M); and the ending 5′ -> 3′ episodic character is stabilizing isotropy stabilized mono mesotropy (E). For S100A14, the middle 3′ -> 5′ episodic character is mesotropy reverse stabilizing isotropy (M), and mesotropy reverse stabilizing isotropy (M). S100A14 is a (7) SEB Episode 3 gene (Table 1).

For S100A14, there are four final MSEBs and there are three final ASEBs (Figure 15). For S100A14, the integrated uppmsebssiwa is 21,523 at Episode 3 (h = 4) and the integrated uppasebssiwa is 8033 at Episode 3 (d = 3); and the integrated dppmsebssiwa is 53,204 at Episode 3 (h = 4) and the integrated dppasebssiwa is 188,934 at Episode 3 (d = 3). For S100A14, the uppesebssiwaa is 14,778 and the dppesebssiwaa is 121,069 that results in an esebssiwaagoT Q of 0.12 at Episode 3. S100A14 meets the threshold of < 0.25 for an infra-pressuromodulated gene (Table 2 & Supplementary file 3 – Supplementary Table S3).

 

≤11,864 gene base category,

>265,005 <607,463 gene base category, ABCB1

For ABCB1, the beginning 5′ -> 3′ episodic character is stabilizing isotropy stabilized, reverse stabilizing isotropy stabilized, reverse stabilizing isotropy stabilized and stabilizing isotropy stabilized mono mesotropy (B) followed by tri anisotropy (B); the middle 5′ -> 3′ episodic character is dual mesotropy (M), mono anisotropy (M), mono mesotropy (M), tri anisotropy (M), mono mesotropy (M) followed by stabilizing isotropy and reverse stabilizing isotropy stabilized mono mesotropy (M); and the ending 5′ -> 3′ episodic character is stabilizing isotropy converted anisotropy-to-mesotropy (E) followed by dual mesotropy (E). For ABCB1, the beginning 3′ -> 5′ episodic character is mesotropy reverse stabilizing isotropy (B) and mesotropy reverse stabilizing isotropy (B); and the middle 3′ -> 5′ episodic character is mesotropy reverse stabilizing isotropy (M). ABCB1 is a [9(-2): 7] SEB Episode 4 gene (Table 1).

For ABCB1, there are four final MSEBs and there are three final ASEBs (Figure 16). For ABCB1, the integrated uppmsebssiwa is 74,163 at Episode 4 (h = 4) and the integrated uppasebssiwa is 18,256 at Episode 4 (d = 3); and the integrated dppmsebssiwa is 161,925 at Episode 4 (h = 4) and the integrated dppasebssiwa is 355,477 at Episode 4 (d = 3). For ABCB1, the uppesebssiwaa is 46,210 and the dppesebssiwaa is 258,701 that results in an esebssiwaagoT Q of 0.18 at Episode 4. ABCB1 meets the threshold of < 0.25 for an infra-pressuromodulated gene (Table 2 & Supplementary file 3 – Supplementary Table S3>).

 

>265,005 <607,463 gene base category,

≥ 607,463 < 2,241,933 gene base category, FOXP2

For FOXP2, the beginning 5′ -> 3′ episodic character is reverse stabilizing isotropy converted mono mesotropy-to-stabilizing isotropy and stabilized mono mesotropy (B) followed by mono anisotropy (B); the middle 5′ -> 3′ episodic character is tri mesotropy (M), multi (4) anisotropy (M), dual mesotropy (M), mono anisotropy (M), stabilizing isotropy stabilized mono mesotropy (M), mono mesotropy (M), mono anisotropy (M), dual mesotropy (M) followed by tri anisotropy (M); and the ending 5′ -> 3′ episodic character is mono mesotropy (E). For FOXP2, the beginning 3′ -> 5′ episodic character is mesotropy reverse stabilizing converting isotropy (B). FOXP2 is a (11) SEB Episode 5 gene (Table 1).

For FOXP2, there are six final MSEBs and there are five final ASEBs (Figure 17). For FOXP2, the integrated uppmsebssiwa is 69,583 at Episode 5 (h = 6) and the integrated uppasebssiwa is 15,948 at Episode 5 (d = 5); and the integrated dppmsebssiwa is 140,583 at Episode 5 (h = 6) and the integrated dppasebssiwa is 273,470 at Episode 5 (d = 5). For FOXP2, the uppesebssiwaa is 42,754 and the dppesebssiwaa is 207,027 that results in an esebssiwaagoT Q of 0.21 at Episode 5. FOXP2 meets the threshold of < 0.25 for an infra-pressuromodulated gene (Table 2; Supplementary file 3 – Supplementary Table S3).

 

≥607,463 <2,241,933 gene base category,

≥ 2,241,933 gene base category, DMD

For DMD, the beginning 5′ -> 3′ episodic character is mono anisotropy (B), mono mesotropy (B) followed stabilizing isotropy and tempered considered (TC) part-reverse stabilizing isotropy stabilized mono mesotropy (B); the middle 5′ -> 3′ episodic character is tri anisotropy (M), stabilizing isotropy stabilized mono mesotropy (M), mono mesotropy (M), dual anisotropy (M), mono mesotropy (M), stabilizing isotropy stabilized mono anisotropy (M), multi (6) anisotropy (M), mono mesotropy (M), mono anisotropy (M), mono mesotropy (M), mono anisotropy (M) followed by mono mesotropy (M); and the ending 5′ -> 3′ episodic character is mono anisotropy (E). For DMD, the beginning 3′ -> 5′ episodic character is mesotropy reverse stabilizing isotropy (B), reverse anisotropy (B) and reverse anisotropy (B). DMD is a (13) SEB Episode 6 gene (Table 1).

For DMD, there are six final MSEBs, and there are seven final ASEBs. The tempered considered (TC) 3′ -> 5′ reverse isotropy point (253,856, 280,037) of first MSEBS is upstream intergene distance 0.125-factor adjusted to 31,732, 31,732 instead of upstream intergene distance 0.25-factor adjusted to 63,464, 63,464 as there are two immediately preceding reverse anisotropy points (167,442, 830,657; 5,488, 272,663) of sufficient 3′ -> 5′ reverse anisotropy to diminish the 3′ -> 5′ reverse isotropy stabilizing effect of 253,856, 280,037 to 31,732, 31,732 (Figure 18). For DMD, the integrated uppmsebssiwa is 74,292 at Episode 6 (h = 6) and the integrated uppasebssiwa is 32,973 at Episode 6 (d = 7); and the integrated dppmsebssiwa is 163,570 at Episode 6 (h = 6) and the integrated dppasebssiwa is 296,028 at Episode 6 (d = 7). For DMD, the uppesebssiwaa is 53,632 and the dppesebssiwaa is 229,799 that results in an esebssiwaagoT Q of 0.23 at Episode 6. DMD meets the threshold of < 0.25 for an infra-pressuromodulated gene (Table 2 & Supplementary file 3 – Supplementary Table S3).

 

≥2,241,933 gene base category,

Filled green squares with yellow border interconnected by arrowed line, 3′ -> 5′ reverse isotropy point (253,856, 280,037) of the tempered considered (TC) first MSEBS upstream intergene distance 0.125-factor adjusted to 31,732, 31,732 instead of upstream intergene distance 0.25-factor adjusted to 63,464, 63,464 as there are two immediately preceding reverse anisotropy points (167,442, 830,657; 5,488, 272,663) of sufficient 3′ -> 5′ reverse anisotropy (Green stars) to diminish the 3′ -> 5′ reverse isotropy stabilizing effect of 253,856, 280,037 to 31,732, 31,732; Filled blue square with yellow border, first MSEBS with 0.125-factor adjusted 31,732, 31,732 point.

Discussion

5′ -> 3′ direction paired point tropy quotients (prpT Qs) for characterization of intergene distance pair SEB episodicity

The 3′ -> 5′ and 5′ -> 3′ direction paired point tropy quotients (prpT Qs) represent the point-by-point 3′ -> 5′ and 5′ -> 3′ direction upstream and downstream intergene distance pair tropies from the gene of interest, respectively, to achieve the nth order of 5′ -> 3′ direction intergene distance pair tropies for the initial number of SEBs to establish the episodicity per gene category.

The transcribing 5′ -> 3′ direction intergene segment pair tropies are necessary to establish the initial anisotropic (single point, dual point, triple point or multiple point SEB; each prpT Q point of SEB < 0.25) and mesotropic (single point, dual point, triple point or multiple point SEB; each prpT Q point ≥ 0.25 < 0.75) periodicity for determination of the number SEBs for the gene of interest, five initial SEBs for Episode 2 category genes, seven initial SEBs for Episode 3 category genes, nine initial SEBs for Episode 4 category genes, 11 initial SEBs for Episode 5 category genes and 13 initial SEBs for Episode 6 category genes.

Upon establishment of the initial subepisodic block episodicity, there is further consideration of:

The instances where there are preceding transcribing 5′ -> 3′ direction stabilizing isotropy prpT Qs (5′ -> 3′ stIsotropy prpT Qs ≥ 0.75), as 0.25 factor-adjusted 5′ -> 3′ direction stabilizing isotropies for part-dependent contribution to increasing the magnitude of tropy effect of the immediately following prpT Q point of the following SEB, in which case the affected prpT Q point of the SEB may or may not remain anisotropic (anisotropy-to-mesotropy converted tropy) or mesotropic (mesotropy-to-stabilizing isotropy converted tropy) (initial SEB +/- 2 per interconversion); and of;

The instances where there are preceding nontranscribing 3′ -> 5′ direction reverse stabilizing isotropy prpT Qs (3′ -> 5′ stIsotropy prpT Qs ≥ 0.75), either as 0.25 factor-adjusted for immediately preceding 3′ -> 5′ direction reverse stabilizing isotropy (ies) for part-dependent contribution to increasing the magnitude of tropy effect of the immediately following prpT Q point of the following SEB, or as a 0.125 factor-adjusted for interposed preceding 3′ -> 5′ direction reverse stabilizing isotropy within a series of 3′ -> 5′ reverse anisotropy prpT Qs (3′ -> 5′ prpT Qs < 0.25) for less that part-dependent contribution to increasing the magnitude of tropy effect of the immediately following prT Q point of the following SEB, in which case the affected SEB also may or may not remain anisotropic (anisotropy-to-mesotropy converted tropy) or mesotropic (mesotropy-to-stabilizing isotropy converted tropy) (initial SEB +/- 2 per inter-conversion).

The transcribing 5′ -> 3′ direction intergene segment pair tropy method establishes the initial number of SEBs, and excludes the number of SEB interconversions and the final number of SEBs, based on which the initial number of episodes for a gene of interest can be determined with certainty (i.e., five initial SEBs = 2 episodes for Episode 2 category genes).

Final 5′ -> 3′ direction episodic sub-episode block sums split-integrated weighted average-averaged gene overexpression tropy quotient (esebssiwaagoT) for supra-pressuromodulated & infra-pressuromodulated genes

The final 5′ -> 3′ direction episodic sub-episode block sums split-integrated weighted average-averaged gene overexpression tropy quotient (esebssiwaagoT) represents for example:

The serially split-integrated averaged anisotropic part SEB sums (ASEBS) to the n th anisotropic SEBS (i.e., anisotropic SEBS 1 + anisotropic SEBS 2 + anisotropic SEBS 3/3 = the third split-integrated average anisotropic SEBS [uppasebssiwa, dppasebssiwa]); and

The serially split-integrated averaged mesotropic part SEB sums (MSEBS) to the n th mesotropic SEBS (i.e., mesotropic SEBS 1 + mesotropic SEBS 2/2 = the second split-integrated average mesotropic SEBS) (uppmsebssiwa, dppmsebssiwa), respectively; thereafter,

The uppasebssiwa and the uppasebssiwa averaged together for the uppesebssiwaa, and the dppasebssiwa and the dppasebssiwa averaged together for the dppesebssiwaa, whereby the uppesebssiwaa/dppesebssiwaa yield the esebssiwaagoT at the Episode 2 fifth SEB, which would be the SEB count in the case of a non-converted Episode 2 category gene. As indicated above, in the case of both the anisotropic intergene distance segment SEB sums (ASEBS) and the mesotropic intergene distance segment SEB sums (MSEBS), each of steps prior the final calculation step is done in upstream part (upp-) and downstream part (dpp-) intergene distance segment SEBSs (uppASEBSs, dppASEBSs; uppMSEBSs, dppMSEBSs) (see ‘Methods’ section for detail).

For the >11,864 ≤265,005 gene base category (i.e., SORL1, PDPN, BTG1, HAPLN1, MRC1, ACPP, TGFA, PHLPP1, SELE, CDH11, ZCCHC2), the final esebssiwaagoT Q is to the end of Episode 2, which implies that intermediate genes appear to be most sensitive to the cellular pressuromodulation effect. In contrast, for the ≤ 11,864 gene base category (i.e., S100A2, PRR3, IFI27, S100A14), the final esebssiwaagoT Q is at the end of Episode 3, which implies that smaller genes appear to be less sensitive to cellular pressuromodulation effect. For the > 265,005 < 607,463 gene base category (i.e., ABCB1), the final esebssiwaagoT is at the end of Episode 4; for the ≥ 607,463 < 2,241,933 gene base category (i.e., FOXP2), the final esebssiwaagoT Q is at the end of Episode 5; and for the ≥ 2,241,933 gene base category, the final esebssiwaagoT Q is at the end of Episode 6 (i.e., DMD), which implies that larger genes appear to also be less sensitive to cellular pressuromodulation effect.

The final esebssiwaagoT Q classifies a LEnC overexpressed gene as a supra-pressuromodulated gene (esebssiwaagoT ≥ 0.25 < 0.75) every time and classifies a BMEnC overexpressed gene every time as an infra-pressuromodulated gene (esebssiwaagoT Q < 0.25) (100% sensitivity; 100% specificity), and therefore, is 100% accurate.

Relevance of the final esebssiwaagoT for classification of genes as either supra-pressuromodulated or infra-pressuromodulated

Genes can be classified as either as a supra-pressuromodulated gene (Supra: esebssiwaagoT Q ≥ 0.25 < 0.75) or as an infra-pressuromodulated gene (Infra: esebssiwaagoT Q < 0.25) with accuracy.

It can be expected that the expression of a Supra or Infra gene will correlate with the pressuromodulation state of a cell type, in which case the most pressuromodulated cell types should express a Supra gene at the highest level, while the least pressuromodulated cell types should express a Supra gene at the lowest level; whereas, the least pressuromodulated cell types should express an Infra gene at the highest level, while the most pressuromodulated cell type should express an Infra gene at the lowest level. This being the case, all Supra genes will be overexpressed in response to increases in cell membrane pressuromodulation, while being underexpressed in response to decreases in cell membrane pressuromodulation; and all Infra genes will be overexpressed in response to decreases in cell membrane pressuromodulation, while being underexpressed in response to increases in cell membrane pressuromodulation. It can be further postulated that there is a graded decrease in the pressuromodulation state of the cell in the progression from zygote (spermatocyte oocyte fusion) totipotency-to-pluripotency-to-differentiation, in which case Supra gene expression would be gradedly lesser in the spectrum toward differentiation away from pluripotency including in the case of Supra gene quintessential Supra transcription factor adapter gene expression, while Infra gene expression would be gradedly greater in the spectrum toward differentiation away from pluripotency including in the case of Infra gene quintessential Infra transcription factor adapter gene expression.

Based on the methodology of this research study all genes can be classified as either Supra (esebssiwaagoT Q ≥ 0.25 < 0.75) or Infra (esebssiwaagoT Q < 0.25) with accuracy. It is further envisioned that early passage primary cells can be rank-ordered by cell pressuromodulation state with additional knowledge of Supra and Infra gene expression level differences between cell types, in which case limiting Supra and Infra transcription factor gene and the limiting Supra and Infra transcription factor adapter gene expression differences between cell types could provide further valuable insight into cell lineage fates.

Conclusion

Based on the findings of this study, an infra-pressuromodulated gene (Infra: esebssiwaagoT Q < 0.25) requires lesser cellular pressuromodulation to be overexpressed, that is, to become optimally horizontally aligned for transcription, in contrast to a supra-pressuromodulated gene (Supra: esebssiwaagoT Q ≥ 0.25 < 0.75) that requires greater cellular pressuromodulation to be overexpressed, that is, to become optimally horizontally aligned for transcription, when an infra-pressuromodulated gene becomes less than optimally horizontally aligned. Therefore, horizontal alignment of 5′ -> 3′ direction intergene distance segment tropy with respect to the gene is the conserved basis for DNA transcription for genes in the pressuromodulated state. This finding is ubiquitously applicable, as it would, for example, also be the basis for viral DNA or RNA stand replication and transcription, for viral DNA or RNA strand transfection vector expression upon integration into the host genome, and for circular bacterial plasmid gene expression, in which case there is gravitational parallel horizontal walking analogous to ‘a rodent on a Ferris Wheel.’

Future perspective

Based on the findings of this study, the final 5′ -> 3′ esebssiwaagoT Q accurately classifies a gene as either a supra-pressuromodulated gene (Supra: esebssiwaagoT Q ≥ 0.25 < 0.75) every time or an infra-pressuromodulated gene (Infra: esebssiwaagoT Q < 0.25) every time (100% sensitivity; 100% specificity), and therefore, is 100% accurate. Therefore, it now becomes possible to classify every gene as either Supra or Infra by applying the esebssiwaagoT Q, without the need for additional experimental data from cells on opposite ends of the pressuromodulation spectrum.

It can be further postulated that in the multicellular organism, the fact that a wide-spectrum of cell types exist in the biological system is entirely attributable to cell membrane pressuromodulation-mediated differences across cell types in Supra and Infra gene expression levels. As such, with a priori knowledge of whether a gene is either a Supra or an Infra gene, it would be possible to rank order the entire spectrum of cell types of the multicellular biological system, ranging from pluripotent-to-differentiated (more pressuromodulated normal state-to-less pressuromodulated normal state), as well as those ranging from normal-to-neoplastic (less pressuromodulated normal state-to-more pressuromodulated abnormal state) based on ‘pressuromodulation state indices’ with cDNA microarray-based Supra gene mRNA expression levels and Infra gene mRNA expression levels for a given cell type (Supra-to-Infra index) as well as the same for different cell types (Supra-to-Supra and Infra-to-Infra indices). With such knowledge it will become easy to appreciate that, in fact, cellular pressuromodulation state-mediated changes in Supra and Infra gene expression levels is the likely basis for the wide-spectrum of cellular differentiation in the multicellular biological system as well as the basis for the maintenance of the neoplastic state.

Comparative cell types at opposite ends of the cell pressuromodulation spectrum include, for example, the lymphatic endothelial cell (LEnC) is a mitogenic without division cell, which is an over-pressuromodulated cell, while the blood microvascular capillary endothelial cell (BMEnC) is non-mitogenic cell, which is an under-pressuromodulated cell; and the multi-nucleated giant cell is also an over-pressuromodulated cell, while the macrophage (mono-nucleated) is an under-pressuromodulated cell, both model cell type-pairs for comparing cell type cDNA microarray mRNA expression levels.

Seven sets of most differentially overexpressed LEnC and BMEnC genes (nonadjusted > twofold) and two sets of juxtaposed lesser differentially overexpressed LEnC and BMEnC genes (nonadjusted one- to two-fold) were selected from a published open access dataset. For these 18 genes, all of the transcribed loci base locations, both protein coding and noncoding, were mined online. The nontranscribing intergene distances were determined upstream and downstream for each gene wrt gene. The transcribing 3′ -> 5′ direction and 5′ -> 3′ prpT Qs (fract) were determined, as were the number of initial anisotropic and mesotropic sub-episode blocks (ASEB, MSEB) for each gene categorized by number of bases [>11,864 ≤265,005 (five sub-episode blocks, 5 SEBs); Episode 2]; ≤11,864 (seven SEBs; Episode 3); >265,005 <607,463 (nine SEBs; Episode 4); ≥ 607,463 < 2,241,933 (11 SEBs; Episode 5); ≥2,241,933 (13 SEBs; Episode 6)]. The 5′ -> 3′ upstream part anisotropic sub-episode block sums (uppASEBS) split-integrated weighted average (uppasebssiwa), the 5′ -> 3′ downstream part anisotropic sub-episode block sums (dppASEBS) split-integrated weighted average (dppasebssiwa), the 5′ -> 3′ upstream part mesotropic sub-episode block sums (uppMSEBS) split-integrated weighted average (uppmsebssiwa), and the 5′ -> 3′ downstream part mesotropic sub-episode block sums (dppMSEBS) split-integrated weighted average (dppmsebssiwa) were determined, based on which the final 5′ -> 3′ upstream part episodic sub-episode block sums split-integrated weighted average-average (uppesebssiwaa) and the final 5′ -> 3′ downstream part episodic sub-episode block sums split-integrated weighted average-average (dppesebssiwaa) and were determined, whereby the final complete episodic sub-episode block sums split-integrated weighted average-averaged gene overexpression tropy quotient (final complete  esebssiwaagoT Q) for each gene per category was determined. The 5′ -> 3′ uppASEBS (y-axis), dppASEBS (x-axis) [ASEBS], uppMSEBS (y-axis) and dppMSEBS (x-axis) [MSEBS], and the final 5′ -> 3′ uppesebssiwaa (y-axis) and dppesebssiwaa (x-axis) [final complete 5′ -> 3′ esebssiwaagoT Q] were log plotted for each gene.

The final 5′ -> 3′ esebssiwaagoT Q classifies a LEnC overexpressed gene as a supra-pressuromodulated gene (esebssiwaagoT Q ≥ 0.25 < 0.75) every time and classifies a BMEnC overexpressed gene every time as an infra-pressuromodulated gene (esebssiwaagoT Q < 0.25) (100% sensitivity; 100% specificity), therefore a methodology that is 100% accurate.

An infra-pressuromodulated gene (Infra: esebssiwaagoT Q < 0.25) requires lesser cellular pressuromodulation to be overexpressed, that is, to become optimally horizontally aligned for transcription, in contrast to a supra-pressuromodulated gene (Supra: esebssiwaagoT Q ≥ 0.25 < 0.75) that requires greater cellular pressuromodulation to be overexpressed, that is, to become optimally horizontally aligned for transcription, when an infra-pressuromodulated gene becomes less than optimally horizontally aligned.

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Click here for additional data file.

Click here for additional data file.