Background
Methods
Identification of DEGs
Gene ontology and pathway enrichment analysis of DEGs
Integration of protein-protein interaction network and modules selection
Prediction of stem loop miRNAs for hub genes
Negatively correlated stem loop miRNA of hub genes in gastric cancer
Prediction of transcription factor for DEGs
Survival analysis of DEGs
Results
Identification of DEGs
GO term and KEGG pathway enrichment analysis of DEGs
Expression | Term/gene function | Gene count | P value |
---|---|---|---|
Upregulation | GO:0001568~blood vessel development | 9 | 3.68E-06 |
GO:0001944~vasculature development | 9 | 6.21E-06 | |
GO:0030198~extracellular matrix organization | 6 | 2.43E-05 | |
GO:0043062~extracellular structure organization | 6 | 2.51E-05 | |
GO:0030199~collagen fibril organization | 4 | 3.97E-05 | |
GO:0010033~response to organic substance | 13 | 6.13E-05 | |
GO:0051291~protein heterooligomerization | 4 | 7.68E-05 | |
GO:0071230~cellular response to amino acid stimulus | 4 | 8.34E-05 | |
GO:0072358~cardiovascular system development | 9 | 1.17E-04 | |
GO:0072359~circulatory system development | 9 | 1.17E-04 | |
Downregulation | GO:0006813~potassium ion transport | 4 | 5.11E-04 |
GO:0010107~potassium ion import | 3 | 7.71E-04 | |
GO:0019731~antibacterial humoral response | 3 | 1.13E-03 | |
GO:0019730~antimicrobial humoral response | 3 | 1.46E-03 | |
GO:0042742~defense response to bacterium | 4 | 2.80E-03 | |
GO:0015672~monovalent inorganic cation transport | 4 | 4.94E-03 | |
GO:0002803~positive regulation of antibacterial peptide production | 2 | 5.18E-03 | |
GO:0002760~positive regulation of antimicrobial humoral response | 2 | 5.18E-03 | |
GO:0002786~regulation of antibacterial peptide production | 2 | 5.18E-03 | |
GO:0002225~positive regulation of antimicrobial peptide production | 2 | 5.18E-03 |
Expression | Term | Count | P value |
---|---|---|---|
Upregulation | hsa04512: ECM-receptor interaction | 7 | 8.90E-08 |
hsa04510: Focal adhesion | 7 | 1.46E-05 | |
hsa04974: Protein digestion and absorption | 5 | 7.37E-05 | |
hsa04151: PI3K-Akt signaling pathway | 7 | 2.25E-04 | |
hsa05146: Amoebiasis | 4 | 3.00E-03 | |
hsa04670: Leukocyte transendothelial migration | 4 | 4.16E-03 | |
hsa04514: Cell adhesion molecules (CAMs) | 4 | 5.92E-03 | |
Downregulation | hsa04971: Gastric acid secretion | 7 | 1.64E-08 |
hsa04966: Collecting duct acid secretion | 3 | 2.12E-03 |
PPI network construction and modules selection
Term | Count | P value |
---|---|---|
hsa04512: ECM-receptor interaction | 7 | 3.05E-10 |
hsa04510: Focal adhesion | 7 | 5.86E-08 |
hsa04151: PI3K-Akt signaling pathway | 7 | 1.07E-06 |
hsa04974: Protein digestion and absorption | 5 | 2.63E-06 |
hsa05146: Amoebiasis | 4 | 2.91E-04 |
hsa04611: Platelet activation | 3 | 1.15E-02 |
MiRNA-hub genes pairs
Gene | Predicted miRNA | Total |
---|---|---|
COL1A1 | hsa-let-7d hsa-miR-98 hsa-let-7a hsa-let-7 g hsa-let-7i | 149 |
COL1A2 | hsa-miR-29c hsa-let-7c hsa-miR-25 hsa-miR-29a hsa-miR-29b | 91 |
COL3A1 | hsa-miR-29b hsa-let-7 g hsa-let-7f hsa-let-7i hsa-let-7a | 85 |
COL4A1 | hsa-miR-29a hsa-miR-29b hsa-miR-29c hsa-miR-148a hsa-let-7c | 118 |
COL6A3 | hsa-miR-29c hsa-miR-29a hsa-miR-29b hsa-miR-206 hsa-miR-330-3p | 108 |
MMP7 | hsa-miR-297 hsa-miR-641 hsa-miR-19b hsa-miR-122 hsa-miR-380 | 32 |
SERPINH1 | hsa-miR-200b hsa-miR-24 hsa-miR-346 hsa-miR-561 hsa-miR-637 | 56 |
SPARC | hsa-miR-29a hsa-miR-299-3p hsa-miR-29c hsa-miR-203 hsa-miR-29b | 206 |
SPP1 | hsa-miR-220b hsa-miR-127-5p hsa-miR-181c hsa-miR-181a hsa-miR-181b | 72 |
THBS2 | hsa-miR-607 hsa-miR-891b hsa-miR-616 hsa-miR-519a hsa-miR-221 | 184 |
TIMP1 | hsa-miR-484 hsa-miR-892a hsa-miR-1293 hsa-miR-1292 | 4 |
VCAN | hsa-miR-203 hsa-miR-144 hsa-miR-632 hsa-miR-135b hsa-miR-136 | 57 |
Gene | Screening stem loop miRNAs | Total |
---|---|---|
COL1A1 | hsa-miR-378 hsa-miR-144 hsa-miR-29c hsa-miR-7 hsa-miR-556 | 21 |
COL1A2 | hsa-let-378 hsa-miR-144 hsa-miR-7 hsa-miR-556 hsa-miR-200c | 32 |
COL3A1 | hsa-miR-7 hsa-miR-556 hsa-miR-378 hsa-miR-200c hsa-miR-18a | 44 |
COL4A1 | hsa-miR-222 hsa-miR-429 hsa-miR-96 hsa-miR-33b hsa-miR-556 | 23 |
COL6A3 | hsa-miR-200c hsa-miR-96 hsa-miR-7 hsa-miR-592 hsa-miR-200a | 38 |
MMP7 | hsa-miR-378 hsa-miR-503 hsa-miR-19a hsa-miR-301b hsa-miR-509 | 11 |
SERPINH1 | hsa-miR-101 hsa-miR-29c hsa-miR-378 hsa-miR-195 | 4 |
SPARC | hsa-miR-7 hsa-miR-378 hsa-miR-18a hsa-miR-19a hsa-miR-96 | 38 |
SPP1 | hsa-miR-29c hsa-miR-139 hsa-miR-195 hsa-miR-101 hsa-miR-129 | 6 |
THBS2 | hsa-miR-144 hsa-miR-378 hsa-miR-7 hsa-miR-200c hsa-miR-592 | 39 |
VCAN | hsa-miR-378 hsa-miR-556 hsa-miR-200c hsa-miR-7 hsa-miR-96 | 38 |
Genes | Negatively correlated stem loop miRNAs | Total |
---|---|---|
COL1A1 | hsa-miR-378 hsa-miR-29c hsa-miR-592 hsa-miR-30c hsa-miR-19a hsa-miR-18a hsa-miR-96 hsa-miR-802 hsa-miR-101 hsa-miR-182 hsa-miR-577 hsa-miR-335 hsa-miR-877 hsa-miR-130b hsa-miR-33b | 15 |
COL1A2 | hsa-miR-7 hsa-miR-200c hsa-miR-19a hsa-miR-96 hsa-miR-200a hsa-miR-200b hsa-miR-429 hsa-miR-29c hsa-miR-130b hsa-miR-30c hsa-miR-182 hsa-miR-194 hsa-miR-301b hsa-miR-335 hsa-miR-577 hsa-miR-1304 hsa-miR-105 hsa-miR-196a hsa-miR-579 hsa-miR-9 hsa-miR-135b | 21 |
COL3A1 | hsa-miR-200c hsa-miR-96 hsa-miR-144 hsa-miR-200a hsa-miR-200b hsa-miR-429 hsa-miR-130b hsa-miR-877 hsa-miR-192 hsa-miR-182 hsa-miR-33b hsa-miR-301b hsa-miR-577 hsa-miR-335 hsa-miR-30c-2* hsa-miR-1304 hsa-miR-29c hsa-miR-206 | 22 |
COL4A1 | hsa-miR-429 hsa-miR-96 hsa-miR-33b hsa-miR-556 hsa-miR-200b hsa-miR-200c hsa-miR-182 hsa-miR-18a hsa-miR-29c hsa-miR-19a hsa-miR-301b hsa-miR-192 hsa-miR-335 hsa-miR-378 hsa-miR-130b | 15 |
COL6A3 | hsa-miR-509-3p hsa-miR-549 hsa-miR-509-3p hsa-miR-29c hsa-miR-605 hsa-miR-579 hsa-miR-206 hsa-miR-1304 hsa-miR-135b hsa-miR-33b hsa-miR-30c hsa-miR-335 hsa-miR-194 hsa-miR-301b hsa-miR-877 hsa-miR-378 hsa-miR-130b hsa-miR-19a hsa-miR-96 | 19 |
MMP7 | hsa-miR-19a | 1 |
SERPINH1 | hsa-miR-30c hsa-miR-195 hsa-miR-378 hsa-miR-29c | 2 |
SPARC | hsa-miR-579 hsa-miR-605 hsa-miR-135b hsa-miR-215 hsa-miR-767-3p hsa-miR-105 hsa-miR-206 hsa-miR-196a hsa-miR-33b hsa-miR-335 hsa-miR-30c hsa-miR-592 hsa-miR-1304 hsa-miR-101 hsa-miR-182 hsa-miR-222 hsa-miR-188-3p hsa-miR-192 hsa-miR-877 hsa-miR-29c hsa-miR-144 hsa-miR-200a hsa-miR-200c hsa-miR-200b hsa-miR-96 hsa-miR-19a hsa-miR-18a hsa-miR-378 | 28 |
SPP1 | hsa-miR-195 hsa-miR-101 | 2 |
THBS2 | hsa-miR-509 hsa-miR-504 hsa-miR-767 hsa-miR-579 hsa-miR-509 hsa-miR-135b hsa-miR-335 hsa-miR-196a hsa-miR-101 hsa-miR-33bhsa-miR-577 hsa-miR-802 hsa-miR-29c hsa-miR-222 hsa-miR-301b hsa-miR-188 hsa-miR-182 hsa-miR-30c hsa-miR-194 hsa-miR-877hsa-miR-192 hsa-miR-130b hsa-miR-206 hsa-miR-429 hsa-miR-96 hsa-miR-19a hsa-miR-200b hsa-miR-18a hsa-miR-486 hsa-miR-556 hsa-miR-592 hsa-miR-200c hsa-miR-144 | 33 |
VCAN | hsa-mir-605 hsa-mir-135b hsa-mir-579 hsa-mir-33b hsa-mir-206 hsa-mir-192 hsa-mir-222 hsa-mir-200b hsa-mir-429 hsa-mir-200a hsa-mir-19a hsa-mir-144 hsa-mir-18a hsa-mir-200c | 14 |
Transcription factors-hub genes pairs
TFs | Genes | Total |
---|---|---|
AR | SPARC COL6A3 SERPINH1 COL4A1 VCAN | 5 |
NANOG | SPARC SPP1 SERPINH1 COL3A1 VCAN | 5 |
SOX2 | SPARC SPP1 COL4A1 VCAN SERPINH1 | 5 |
EP300 | SPARC COL4A1 VCAN SERPINH1 | 4 |
PPARG | SPARC SPP1 SERPINH1 COL3A1 | 4 |
SALL4 | SPP1 COL4A1 VCAN SERPINH1 | 4 |
TCF3 | SPARC SPP1 VCAN SERPINH1 | 4 |
EZH2 | COL4A1 VCAN COL6A3 | 3 |
FLI1 | SPARC SERPINH1 COL6A3 | 3 |
FOXP1 | SPP1 VCAN COL6A3 | 3 |
GATA2 | SPARC SPP1 SERPINH1 | 3 |
HSF1 | SPARC SERPINH1 COL6A3 | 3 |
NFE2L2 | SPARC COL4A1 VCAN | 3 |
NR1H3 | SPP1 COL4A1 COL6A3 | 3 |
POU3F2 | SPP1 VCAN COL3A1 | 3 |
POU5F1 | SPARC SPP1 VCAN | 3 |
PRDM14 | SPARC SPP1 VCAN | 3 |
RUNX1 | SPARC SPP1 COL6A3 | 3 |
RUNX2 | SPARC VCAN COL6A3 | 3 |
SMAD4 | VCAN COL6A3 COL3A1 | 3 |
SPI1 | SPARC SPP1 SERPINH1 | 3 |
SUZ12 | COL4A1 VCAN SERPINH1 | 3 |
TCF4 | COL4A1 VCAN COL6A3 | 3 |
TP53 | COL4A1 VCAN COL6A3 | 3 |
TP63 | SPARC COL4A1 SERPINH1 | 3 |