| Literature DB >> 28856086 |
Congjian Liu1, Xiang Gu1, Zhenxian Jiang1.
Abstract
More than one pathway is involved in disease development and progression, and two or more pathways may be interconnected to further affect the disease onset, as functional proteins participate in multiple pathways. Thus, identifying cross-talk among pathways is necessary to understand the molecular mechanisms of multiple myeloma (MM). Based on this, this paper looked at extracting potential pathway cross-talk in MM through an integrative approach using Monte Carlo cross-validation analysis. The gene expression library of MM (accession number: GSE6477) was downloaded from the Gene Expression Omnibus (GEO) database. The integrative approach was then used to identify potential pathway cross-talk, and included four steps: Firstly, differential expression analysis was conducted to identify differentially expressed genes (DEGs). Secondly, the DEGs obtained were mapped to the pathways downloaded from an ingenuity pathways analysis (IPA), to reveal the underlying relationship between the DEGs and pathways enriched by these DEGs. A subset of pathways enriched by the DEGs was then obtained. Thirdly, a discriminating score (DS) value for each paired pathway was computed. Lastly, random forest (RF) classification was used to identify the paired pathways based on area under the curve (AUC) and Monte Carlo cross-validation, which was repeated 50 times to explore the best paired pathways. These paired pathways were tested with another independently published MM microarray data (GSE85837), using in silico validation. Overall, 60 DEGs and 19 differential pathways enriched by DEGs were extracted. Each pathway was sorted based on their AUC values. The paired pathways, inhibition of matrix metalloproteases and EIF2 signaling pathway, indicated the best AUC value of 1.000. Paired pathways consisting of IL-8 and EIF2 signaling pathways with higher AUC of 0.975, were involved in 7 runs. Furthermore, it was validated consistently in separate microarray data sets (GSE85837). Paired pathways (inhibition of matrix metalloproteases and EIF2 signaling, IL-8 signaling and EIF2 signaling) exhibited the best AUC values and higher frequency of validation. Two paired pathways (inhibition of matrix metalloproteases and EIF2 signaling, IL-8 signaling and EIF2 signaling) were used to accurately classify MM and control samples. These paired pathways may be potential bio-signatures for diagnosis and management of MM.Entities:
Keywords: Area under the curve; Differentially expressed genes; Monte Carlo cross-validation; Multiple myeloma; Pathway cross-talk
Year: 2017 PMID: 28856086 PMCID: PMC5565744 DOI: 10.1016/j.jbo.2017.08.001
Source DB: PubMed Journal: J Bone Oncol ISSN: 2212-1366 Impact factor: 4.072
List of differentially expressed genes (DEGs).
| RNASE2 | −4.2668 | 1.25E-24 | LMO2 | −2.02467 | 1.26E-04 |
| CLC | −4.94929 | 1.05E-13 | CD24 | −2.24512 | 1.65E-04 |
| PRG3 | −3.90837 | 2.93E-12 | MRC1 | −2.06384 | 2.36E-04 |
| RNASE3 | −4.31871 | 5.08E-12 | CRISP3 | −2.73151 | 2.55E-04 |
| PRG2 | −5.93443 | 1.01E-09 | MS4A3 | −2.17214 | 2.61E-04 |
| MPO | −2.52454 | 8.15E-09 | ZNF358 | 2.042213 | 2.66E-04 |
| DEFA4 | −2.22389 | 1.70E-08 | MS4A6A | −2.21587 | 3.54E-04 |
| ELANE | −4.39842 | 1.94E-08 | IL4R | −2.1392 | 3.74E-04 |
| EPX | −3.18113 | 9.02E-08 | PXDC1 | −2.08509 | 4.67E-04 |
| ARMC7 | 2.314169 | 2.21E-07 | CD320 | 2.241042 | 4.83E-04 |
| CAMP | −3.0549 | 9.82E-07 | CD163 | −2.52643 | 5.17E-04 |
| IGHG1 | −3.7307 | 2.23E-06 | LUM | −3.58203 | 5.20E-04 |
| CTSH | −2.87845 | 3.55E-06 | CXCL8 | −2.40243 | 5.26E-04 |
| AIF1 | −2.16656 | 4.43E-06 | NOD2 | −2.95453 | 5.26E-04 |
| LST1 | −2.19262 | 8.38E-06 | S100A8 | −2.70373 | 5.61E-04 |
| IGLJ3 | −4.49176 | 1.13E-05 | CXCL2 | −2.71229 | 5.61E-04 |
| CLPP | 2.32109 | 1.65E-05 | IGHD | −4.07084 | 5.84E-04 |
| LTF | −3.89554 | 1.65E-05 | HMOX1 | −2.36868 | 5.99E-04 |
| FABP4 | −2.79511 | 3.18E-05 | MS4A4A | −3.38126 | 6.11E-04 |
| LYVE1 | −2.9819 | 3.18E-05 | HIF1A | −2.13129 | 6.18E-04 |
| NRP1 | −2.08155 | 3.34E-05 | VNN2 | −2.4071 | 6.18E-04 |
| S100A12 | −2.16333 | 3.34E-05 | MAFB | −3.4547 | 6.41E-04 |
| CEACAM8 | −3.52708 | 4.20E-05 | ALDH1A3 | −2.01185 | 6.80E-04 |
| IGLV1-44 | −4.8402 | 6.64E-05 | LHFP | −2.18934 | 6.98E-04 |
| KCTD12 | −2.56891 | 6.99E-05 | S100A9 | −2.3273 | 8.20E-04 |
| CD14 | −3.15551 | 7.82E-05 | MNDA | −3.14832 | 9.14E-04 |
| RPS11 | 2.079562 | 8.44E-05 | HLA-DPA1 | −2.64283 | 9.63E-04 |
| IGK | −3.99784 | 9.70E-05 | TGFBI | −2.93660 | 9.89E-04 |
| P2RY13 | −2.46684 | 1.05E-04 | MAGEA4 | 2.361871 | 9.92E-04 |
| DTX2 | 2.071491 | 1.05E-04 | MROH7 | −2.03615 | 9.95E-04 |
FC, fold change; FDR, false discovery rate.
Pathways enriched by differentially expressed genes (DEGs).
| Granulocyte Adhesion and Diapedesis | 6.09E-11 | 163 | 4 |
| EIF2 Signaling | 2.88E-10 | 173 | 6 |
| Atherosclerosis Signaling | 1.32E-07 | 119 | 1 |
| Hepatic Fibrosis / Hepatic Stellate Cell Activation | 1.66E-07 | 137 | 2 |
| LXR/RXR Activation | 1.78E-07 | 121 | 1 |
| T Helper Cell Differentiation | 2.91E-06 | 62 | 3 |
| Bladder Cancer Signaling | 5.83E-06 | 86 | 5 |
| Role of Macrophages | 2.23E-05 | 282 | 4 |
| Complement System | 4.96E-05 | 32 | 3 |
| Altered T Cell and B Cell Signaling in Rheumatoid Arthritis | 6.80E-05 | 76 | 2 |
| IL-8 Signaling | 6.96E-05 | 183 | 1 |
| PI3K Signaling in B Lymphocytes | 1.01E-04 | 122 | 3 |
| Regulation of the Epithelial-Mesenchymal Transition Pathway | 1.17E-04 | 175 | 1 |
| Neuroprotective Role of THOP1 in Alzheimer's Disease | 3.38E-04 | 40 | 1 |
| Role of Osteoblasts | 5.18E-04 | 214 | 2 |
| Acute Myeloid Leukemia Signaling | 5.48E-04 | 76 | 3 |
| ILK Signaling | 7.71E-04 | 181 | 2 |
| Macropinocytosis Signaling | 8.53E-04 | 68 | 2 |
| LPS/IL-1 Mediated Inhibition of RXR Function | 9.14E-04 | 210 | 2 |
FDR, false discovery rate; common gene, the overlap between DEGs and genes in the pathway.
Top 10 pairs of pathways with AUC value.
| Pairs of pathways | AUC |
|---|---|
| (1a) Inhibition of matrix metalloproteases | 1.000 |
| (1b) EIF2 signaling | |
| (2a) IL-8 signaling | 0.975 |
| (2b) EIF2 signaling | |
| (3a) IL-8 signaling | 0.939 |
| (3b) Regulation of eIF4 and p70S6K signaling | |
| (4a) IL-8 signaling | 0.927 |
| (4b) FGF signaling | |
| (5a) PI3K signaling in B lymphocytes | 0.910 |
| (5b) EIF2 signaling | |
| (6a) PI3K signaling in B lymphocytes | 0.900 |
| (6b) FGF signaling | |
| (7a) Colorectal cancer metastasis signaling | 0.898 |
| (7b) EIF2 signaling | |
| (8a) Altered T cell and B cell signaling in rheumatoid arthritis | 0.897 |
| (8b) EIF2 signaling | |
| (9a) Inhibition of matrix metalloproteases | 0.892 |
| (9b) Regulation of eIF4 and p70S6K signaling | |
| (10a) EIF2 signaling | 0.890 |
| (10b) TREM1 signaling |
AUC, area under the curve.
Top 10 pairs of pathways based on occurrence number not less than 5.
| PI3K Signaling in B Lymphocytes; EIF2 Signaling | 27 |
| Inhibition of Matrix Metalloproteases; EIF2 Signaling | 10 |
| PI3K Signaling in B Lymphocytes; Regulation of eIF4 and p70S6K Signaling | 10 |
| Colorectal Cancer Metastasis Signaling; EIF2 Signaling | 8 |
| IL-8 Signaling; EIF2 Signaling | 7 |
| PI3K Signaling in B Lymphocytes; GABA Receptor Signaling | 7 |
| Role of NFAT in Regulation of the Immune Response; EIF2 Signaling | 6 |
| EIF2 Signaling; IL-17A Signaling in Fibroblasts | 6 |
| Granulocyte Adhesion and Diapedesis; EIF2 Signaling | 6 |
| Leukocyte Extravasation Signaling; EIF2 Signaling | 5 |
| EIF2 Signaling; IL-10 Signaling | 5 |
| MSP-RON Signaling Pathway; EIF2 Signaling | 5 |
Top 10 pairs of pathways with AUC value, validated using the other MM microarray data.
| Pairs of pathways | AUC |
|---|---|
| (1a) Inhibition of matrix metalloproteases | 0.971 |
| (1b) EIF2 signaling | |
| (2a) TREM1 signaling | 0.968 |
| (2b) EIF2 signaling | |
| (3a) EIF2 signaling | 0.961 |
| (3b) IL-8 signaling | |
| (4a) IL-10 signaling | 0.956 |
| (4b) EIF2 signaling | |
| (5a) Antigen Presentation Pathway | 0.955 |
| (5b) LPS/IL-1 Mediated Inhibition of RXR Function | |
| (6a) Caveolar-mediated Endocytosis Signaling | 0.955 |
| (6b) Agranulocyte Adhesion and Diapedesis | |
| (7a) Regulation of eIF4 and p70S6K Signaling | 0.953 |
| (7b) Actin Nucleation by ARP-WASP Complex | |
| (8a) Antigen Presentation Pathway | 0.947 |
| (8b) IL-6 Signaling | |
| (9a) PI3K Signaling in B Lymphocytes | 0.945 |
| (9b) GABA Receptor Signaling | |
| (10a) EIF2 Signaling | 0.944 |
| (10b) Actin Cytoskeleton Signaling |
AUC, area under the curve.
Top 10 pairs of pathways based on occurrence number not less than 5, selected from the validated microarray data.
| Caveolar-mediated Endocytosis Signaling; Agranulocyte Adhesion and Diapedesis | 45 |
| EIF2 Signaling; Inhibition of Matrix Metalloproteases | 43 |
| Antigen Presentation Pathway; IL-6 Signaling | 37 |
| EIF2 Signaling; IL-8 Signaling | 31 |
| EIF2 Signaling; Regulation of eIF4 and p70S6K Signaling | 31 |
| Antigen Presentation Pathway; LPS/IL-1 Mediated Inhibition of RXR Function | 21 |
| EIF2 Signaling; IL-17A Signaling in Fibroblasts | 11 |
| EIF2 Signaling; IL-10 Signaling | 9 |
| Regulation of eIF4 and p70S6K Signaling; Actin Nucleation by ARP-WASP Complex | 9 |
| PI3K Signaling in B Lymphocytes; GABA Receptor Signaling | 5 |