| Literature DB >> 22873350 |
Eduardo Tejera1, João Bernardes, Irene Rebelo.
Abstract
BACKGROUND: In this study we explored preeclampsia through a bioinformatics approach. We create a comprehensive genes/proteins dataset by the analysis of both public proteomic data and text mining of public scientific literature. From this dataset the associated protein-protein interaction network has been obtained. Several indexes of centrality have been explored for hubs detection as well as the enrichment statistical analysis of metabolic pathway and disease.Entities:
Mesh:
Year: 2012 PMID: 22873350 PMCID: PMC3483240 DOI: 10.1186/1752-0509-6-97
Source DB: PubMed Journal: BMC Syst Biol ISSN: 1752-0509
Figure 1PPI network and topology. Left) PPI network and Right) Degree distribution. The degree distribution follows a power law distribution.
Top 50 genes obtained by analysis of the PPI network
| 4067 | LYN | 983.5136 | 2324 | FLT4 | 426.74 |
| 2335 | FN1 | 823.9037 | 6767 | ST13 | 425.5747 |
| 29110 | TBK1 | 672.1386 | 873 | CBR1 | 424.257 |
| 8826 | IQGAP1 | 635.9629 | 667 | DST | 414.0964 |
| 1759 | DNM1 | 628.7167 | 9495 | AKAP5 | 412.7567 |
| 5573 | PRKAR1A | 622.5864 | 8601 | RGS20 | 408.6292 |
| 10397 | NDRG1 | 590.672 | 2896 | GRN | 401.0426 |
| 2923 | PDIA3 | 559.3358 | 4323 | MMP14 | 400.1593 |
| 5339 | PLEC | 541.5909 | 55697 | VAC14 | 394.4482 |
| 6303 | SAT1 | 515.6939 | 5228 | PGF | 393.3167 |
| 2321 | FLT1 | 508.3947 | 8553 | BHLHE40 | 392.8039 |
| 2317 | FLNB | 505.1671 | 604 | BCL6 | 385.7928 |
| 4221 | MEN1 | 499.019 | 5054 | SERPINE1 | 382.5547 |
| 7067 | THRA | 487.6884 | 4597 | MVD | 380.0219 |
| 2147 | F2 | 482.7173 | 5569 | PKIA | 377.6185 |
| 3959 | LGALS3BP | 475.7565 | 140885 | SIRPA | 375.9565 |
| 10603 | SH2B2 | 473.9241 | 3624 | INHBA | 367.5795 |
| 7422 | VEGFA | 465.5212 | 10272 | FSTL3 | 367.2976 |
| 8815 | BANF1 | 461.918 | 4846 | NOS3 | 361.5554 |
| 23650 | TRIM29 | 448.6764 | 3553 | IL1B | 357.2569 |
| 7124 | TNF | 441.7007 | 3880 | KRT19 | 355.4412 |
| 904 | CCNT1 | 440.8304 | 9444 | QKI | 354.3211 |
| 3556 | IL1RAP | 430.4483 | 8773 | SNAP23 | 348.0265 |
| 9131 | AIFM1 | 429.2521 | 27250 | PDCD4 | 345.9363 |
| 6449 | SGTA | 429.1609 | 5291 | PIK3CB | 345.5114 |
The table shown the first 50 genes selected according to the score values and arranged in descendent order. We also provide the gene symbol the associated Entrez Gene identifier.
Notes: 1) Entrez gene ID.
Figure 2Communality and clusters analysis. Left) Representation of the largest connected community. Red nodes represent the genes involved in communities overlapping. White nodes represent the bigger community. Right) Representation of C8 and C4 clusters and the related statistically significant biological process obtained by gene ontology enrichment analysis.
The diseases enrichment analysis
| Cancer (p-value = 1.24E-11) | breast cancer | 9.76E-07 |
| ovarian cancer | 4.30E-04 | |
| lupus erythematosus | 4.4E-02 | |
| Cardiovascular (p-value = 4.28E-9) | myocardial infarction | 8.7E-09 |
| coronary artery disease | 7.38E-06 | |
| Stroke | 6.16E-05 | |
| heart disease, ischemic | 9.7E-03 | |
| blood pressure, arterial | 8.2E-03 | |
| inflammatory bowel disease | 2.9E-02 | |
| Aging (p-value = 5.23E-05) | Alzheimer's Disease | 2.36E-07 |
| Longevity | 2.17E-04 | |
| atherosclerosis | 3.7E-02 | |
| Arthritis | 3.60E-02 | |
| Reproduction (p-value = 7.9E-03) | preeclampsia | 1.29E-05 |
| pregnancy loss, recurrent | 6.08E-04 |
The table provides the p-value obtained from disease enrichment analysis according to the Disease Class and also the sub-classes diseases following the GAD database structure. The results showed are partials as discussed in the respective section.
The KEGG pathway enrichment analysis
| Pathways in cancer | 1.10E-42 | Fc gamma R-mediated phagocytosis | 2.90E-07 |
| Focal adhesion | 3.50E-29 | RIG-I-like receptor signaling pathway | 5.30E-07 |
| Apoptosis | 2.10E-17 | Chemokine signaling pathway | 5.90E-07 |
| Neurotrophin signaling pathway | 3.40E-17 | Leukocyte transendothelial migration | 6.20E-07 |
| TGF-beta signaling pathway | 5.10E-16 | VEGF signaling pathway | 8.60E-07 |
| T cell receptor signaling pathway | 8.90E-15 | NOD-like receptor signaling pathway | 1.20E-06 |
| ErbB signaling pathway | 1.80E-14 | mTOR signaling pathway | 7.00E-06 |
| B cell receptor signaling pathway | 8.70E-14 | Complement and coagulation cascades | 7.90E-06 |
| Adherens junction | 2.00E-12 | Tight junction | 1.10E-05 |
| Fc epsilon RI signaling pathway | 3.60E-12 | RNA polymerase | 1.60E-05 |
| ECM-receptor interaction | 6.80E-12 | Ubiquitin mediated proteolysis | 2.20E-05 |
| Insulin signaling pathway | 3.00E-10 | GnRH signaling pathway | 1.10E-04 |
| Regulation of actin cytoskeleton | 3.10E-09 | Hematopoietic cell lineage | 1.20E-04 |
| Toll-like receptor signaling pathway | 1.01E-08 | Cytokine-cytokine receptor interaction | 2.00E-04 |
| Wnt signaling pathway | 1.10E-08 | Hedgehog signaling pathway | 3.70E-04 |
| Cell cycle | 1.50E-08 | Natural killer cell mediated cytotoxicity | 3.80E-04 |
| MAPK signaling pathway | 1.50E-08 | Cytosolic DNA-sensing pathway | 6.70E-04 |
| Adipocytokine signaling pathway | 7.50E-08 | Notch signaling pathway | 2.60E-03 |
| Progesterone-mediated oocyte maturation | 2.50E-07 | Renin-angiotensin system | 1.80E-02 |
The table provides the p-value obtained from pathway enrichment analysis in the KEGG database. The pathways names correspond with the KEGG nomenclature. The results showed are partials as discussed in the respective section.
Figure 3Genes-metabolic pathways interaction. The genes and pathways were selected after hubs detection (see Table 1) and enrichment analysis respectively (see Table 3).
GEO data used for dataset construction
| GSE6573 | 10(PE), 10(N) | Affymetrix | At delivery | Placenta | [ |
| GSE47071 | 10(PE), 4(N) | Agilent | See notes | Placenta | [ |
| GSE25906 | 23(PE), 37(N) | Illumina | 27-38 | Placenta | [ |
| GSE147222 | 12(PE), 11(N) | Affymetrix | See notes | Placenta | [ |
| GSE10588 | 17(PE), 26(N) | ABI Human | At delivery | Placenta | [ |
The Table shown the GEO data sources, references and complementary information used in the study.
Notes: 1) The 10 samples were collected for placenta biopsy during delivery. Five of the preeclamptic samples were collected before 31 weeks of gestation and the rest after this time. 2) The 23 samples were collected for placenta biopsy during delivery, however, because in GEO appear two platform types, both were analysed.