Background
Methods
Microarray data
Data preprocessing and DEGs screening
KEGG pathway enrichment analysis
PPI network construction
Fast Network Component Analysis (FastNCA)
Results
DEGs screening
Contrastive group
|
The number of DEGs
|
The number of up-regulated DEGs
|
The number of down-regulated DEGs
|
---|---|---|---|
HFF1_24 h vs HFF1 | 117 | 103 | 14 |
HFF1_48 h vs HFF1 | 347 | 234 | 113 |
HFF1_72 h vs HFF1 | 557 | 337 | 320 |
ES vs HFF1 | 2263 | 1007 | 1256 |
iPS vs HFF1 | 2307 | 699 | 16 8 |
KEGG pathway enrichment analysis
KEGG pathway
|
Count
|
P value
| ||
---|---|---|---|---|
HFF1_24 h vs HFF1 | Up-regulated gene | hsa04622: RIG-I-like receptor signaling pathway | 6 | 9.35E-05 |
hsa04620: Toll-like receptor signaling pathway | 5 | 0.0043 | ||
hsa04623: Cytosolic DNA-sensing pathway | 4 | 0.0057 | ||
HFF1_48 h vs HFF1 | Up-regulated gene | hsa04620: Toll-like receptor signaling pathway | 6 | 0.0209 |
hsa04622: RIG-I-like receptor signaling pathway | 5 | 0.0249 | ||
Down-regulated gene | hsa05410: Hypertrophic cardiomyopathy (HCM) | 4 | 0.0479 | |
HFF1_72 h vs HFF1 | Up-regulated gene | hsa00330: Arginine and proline metabolism | 6 | 0.0076 |
hsa00480: Glutathione metabolism | 5 | 0.0287 | ||
hsa00250: Alanine, aspartate and glutamate metabolism | 4 | 0.0349 | ||
Down-regulated gene | hsa04510: Focal adhesion | 13 | 4.57E-05 | |
hsa04810: Regulation of actin cytoskeleton | 10 | 0.0056 | ||
hsa05200: Pathways in cancer | 11 | 0.0272 | ||
ES vs HFF1 | Up-regulated gene | hsa05217: Basal cell carcinoma | 14 | 9.58E-06 |
hsa04310: Wnt signaling pathway | 22 | 1.28E-04 | ||
hsa05200: Pathways in cancer | 36 | 2.29E-04 | ||
hsa00330: Arginine and proline metabolism | 10 | 0.0029 | ||
Down-regulated gene | hsa04510: Focal adhesion | 40 | 8.73E-08 | |
hsa00520: Amino sugar and nucleotide sugar metabolism | 13 | 1.09E-04 | ||
hsa04512: ECM-receptor interaction | 18 | 2.52E-04 | ||
hsa04142: Lysosome | 20 | 0.0019 | ||
iPS vs HFF1 | Up-regulated gene | hsa04310: Wnt signaling pathway | 16 | 2.39E-04 |
hsa05217: Basal cell carcinoma | 8 | 0.0029 | ||
hsa00250: Alanine, aspartate and glutamate metabolism | 6 | 0.0041 | ||
hsa00260: Glycine, serine and threonine metabolism | 6 | 0.0041 | ||
Down-regulated gene | hsa04510: Focal adhesion | 56 | 1.46E-11 | |
hsa04512: ECM-receptor interaction | 27 | 3.06E-07 | ||
hsa00520: Amino sugar and nucleotide sugar metabolism | 16 | 2.84E-05 | ||
hsa04810: Regulation of actin cytoskeleton | 42 | 1.43E-04 |
PPI network construction
The number of nodes
|
The number of edges
| |
---|---|---|
HFF1_24 h | 80 | 931 |
HFF1_48 h | 217 | 1290 |
HFF1_72 h | 358 | 1838 |
ES | 1737 | 9067 |
iPS | 1829 | 11765 |
HFF1_24 h
|
HFF1_48 h
|
HFF1_72 h
|
ES
|
iPS
| |||||
---|---|---|---|---|---|---|---|---|---|
Gene
|
Degree
|
Gene
|
Degree
|
Gene
|
Degree
|
Gene
|
Degree
|
Gene
|
Degree
|
ISG15 | 50 | STAT1 | 59 | STAT1 | 52 | TSPO | 206 | TSPO | 224 |
STAT1 | 50 | ISG15 | 51 | ISG15 | 44 | TP53 | 168 | TP53 | 182 |
DDX58 | 48 | IFIT3 | 49 | IRF7 | 41 | CCND1 | 106 | FN1 | 138 |
IFIT3 | 47 | IRF7 | 49 | DDX58 | 40 | CDH1 | 104 | IL6 | 136 |
IRF7 | 47 | DDX58 | 48 | TOP2A | 40 | MYC | 96 | GAPDH | 131 |
MX1 | 47 | IFIT1 | 48 | MX17 | 39 | FGF2 | 87 | CCND1 | 117 |
RTP4 | 46 | IFI35 | 47 | CENPF | 38 | CD44 | 83 | CDK1 | 117 |
IFIH1 | 45 | RTP4 | 47 | KIF2C | 38 | MMP9 | 82 | CDH1 | 108 |
IFIT1 | 45 | MX1 | 47 | ASPM | 38 | COL1A2 | 81 | CD44 | 103 |
IFI35 | 44 | RSAD2 | 45 | IFIT1 | 38 | ALPL | 81 | RAC1 | 96 |
TF activities calculated by FastNCA and correlation with gene expression of TFs
Regulatory network for TFs and DEGs
TF
|
HFF1_24 h
|
HFF1_48 h
|
HFF1_72 h
|
ES
|
iPS
|
---|---|---|---|---|---|
CNTN2 | 1 | 2 | 0 | 2 | 25 |
STAT5B | 1 | 19 | 41 | 245 | 299 |
FOXA3 | 0 | 0 | 2 | 98 | 14 |
FOXF2 | 5 | 5 | 5 | 28 | 25 |
GATA2 | 6 | 7 | 6 | 0 | 1 |
SMAD6 | 0 | 0 | 0 | 0 | 3 |