Background
Methods
Datasets
GEO accession | Author | Platform | Samples(P:N) | Year |
---|---|---|---|---|
GSE7084 | Tromp G | GPL570[HG-U133_Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array;GPL2507Sentrix Human-6 Expression BeadChip | 7:8 | 2007 |
GSE47472 | Biros E | GPL10558Illumina HumanHT-12 V4.0 expression beadchip | 14:8 | 2013 |
GSE57691 | Biros E | GPL10558Illumina HumanHT-12 V4.0 expression beadchip | 49:10 | 2015 |
Analysis of DEGs
Functional annotation analyses of DEGs
PPI network construction
Analysis of potential TFs to target DEGs
Immunohistochemical (IHC) staining for CCR7 and PDGFA
Receiver operating characteristic analyses
Results
DEGs analysis
Gene ID | Gene Symbol | FDR | Combined.ES | Gene ID | Gene Symbol | FDR | Combined.ES |
---|---|---|---|---|---|---|---|
Up-regulated genes | Down-regulated genes | ||||||
115,362 | GBP5 | 2.46E-07 | 1.718728703 | 5154 | PDGFA | 2.01E-10 | −2.16796797 |
3043 | HBB | 5.91E-07 | 1.779962188 | 2063 | NR2F6 | 3.18E-09 | −2.07109705 |
3040 | HBA2 | 1.45E-06 | 1.734233872 | 1459 | CSNK2A2 | 3.18E-09 | −2.009947802 |
3560 | IL2RB | 4.69E-06 | 1.434746719 | 28,999 | KLF15 | 6.12E-09 | −2.026442955 |
4753 | NELL2 | 8.52E-06 | 1.395326 | 7220 | TRPC1 | 7.99E-09 | −1.919770839 |
5743 | PTGS2 | 1.01E-05 | 1.378162107 | 81,493 | SYNC | 2.20E-08 | −1.980299756 |
84,658 | ADGRE3 | 1.03E-05 | 1.423979214 | 7704 | ZBTB16 | 2.31E-08 | −2.023343723 |
8972 | MGAM | 1.37E-05 | 1.372006422 | 116,151 | FAM210B | 4.86E-08 | −1.869732488 |
54,504 | CPVL | 1.49E-05 | 1.4454994 | 2308 | FOXO1 | 4.94E-08 | −1.841528166 |
1236 | CCR7 | 1.66E-05 | 1.335317111 | 58,499 | ZNF462 | 5.47E-08 | −2.004150438 |
Functional and pathway enrichment analyses of DEGs
GO ID | GO term | List in term | Log p |
---|---|---|---|
Biological process | |||
GO:0072359 | circulatory system development | 101/913 | −10.6462 |
GO:0061061 | muscle structure development | 67/563 | −8.4846 |
GO:0006413 | translational initiation | 40/268 | −7.9403 |
GO:0008285 | negative regulation of cell proliferation | 70/643 | −7.2506 |
GO:0060548 | negative regulation of cell death | 89/910 | −6.8694 |
GO:0003170 | heart valve development | 12/34 | −6.8435 |
GO:0007169 | transmembrane receptor protein tyrosine kinase signaling pathway | 89/928 | −6.4948 |
GO:0070372 | regulation of ERK1 and ERK2 cascade | 34/238 | −6.3893 |
GO:0006935 | chemotaxis | 81/860 | −5.6514 |
GO:0060485 | mesenchyme development | 32/237 | −5.5128 |
Molecular function | |||
GO:0016491 | oxidoreductase activity | 75/719 | −6.9626 |
GO:0009055 | electron carrier activity | 21/112 | −6.0854 |
GO:0019904 | protein domain specific binding | 61/623 | −4.9011 |
GO:0008092 | cytoskeletal protein binding | 74/810 | −4.7540 |
GO:0032403 | protein complex binding | 82/928 | −4.6775 |
GO:0003735 | structural constituent of ribosome | 27/210 | −4.3707 |
GO:1,901,681 | sulfur compound binding | 27/232 | −3.6356 |
GO:0016453 | C-acetyltransferase activity | 3/4 | −3.1832 |
GO:0016634 | oxidoreductase activity, acting on the CH-CH group of donors, oxygen as acceptor | 4/9 | −3.0208 |
GO:0008565 | protein transporter activity | 14/98 | −2.9919 |
GO:0016491 | oxidoreductase activity | 75/719 | −6.9626 |
Cellular component | |||
GO:0044429 | mitochondrial part | 109/943 | −12.6878 |
GO:0005925 | focal adhesion | 55/391 | −9.6768 |
GO:0030529 | intracellular ribonucleoprotein complex | 70/710 | −5.6423 |
GO:0005759 | mitochondrial matrix | 45/404 | −5.1349 |
GO:0015629 | actin cytoskeleton | 46/442 | −4.4798 |
GO:0005901 | caveola | 14/76 | −4.1752 |
GO:0030663 | COPI-coated vesicle membrane | 6/17 | −3.6750 |
GO:0044455 | mitochondrial membrane part | 22/173 | −3.6079 |
GO:0090665 | glycoprotein complex | 6/21 | −3.1162 |
GO:0044451 | nucleoplasm part | 59/708 | −2.9012 |
KEGG ID | KEGG term | List in term | Log p | Gene list |
---|---|---|---|---|
hsa03010 | Ribosome | 22/135 | −6.5000 | FAU,RPL7,RPL9,RPL24,RPL27,RPL30,RPL35A,RPS6,RPS21,UBA52,MRPL33,MRPL19,MRPL18,MRPL22,MRPS16,RSL24D1,MRPL20,MRPS15,MRPS6,MRPS5,MRPL1,MRPL24 |
hsa00640 | Propanoate metabolism | 10/32 | −5.9097 | ACAT1,ACAT2,LDHA,LDHB,ALDH6A1,MUT,PCCA,SUCLG2,HIBCH,ACSS2,ALDH2,ALDH3A2,HADH,HMGCL,ACO1,GCSH,HOGA1,ESD,PFKM,PRPS2,PHGDH,L2HGDH |
hsa04510 | Focal adhesion | 23/202 | −4.1028 | ACTN1,CAPN2,CAV2,COL4A1,FLNC,HRAS,ITGA7,LAMA5,LAMC1,PPP1R12A,PDGFA,PDGFRB,MAPK3,PTEN,ROCK1,THBS2,ITGA10,ROCK2,ITGA11,PARVA,PDGFC,TLN2,SHC4,FGF13,MYH10,WASL,ARPC1A,ARHGEF12,GNG12,PIP4K2C |
hsa04270 | Vascular smooth muscle contraction | 16/120 | −3.8133 | ADCY3,AGTR1,CALD1,EDNRA,GNA11,KCNMB1,MYH11,MYL6,PPP1R12A,MAPK3,PTGIR,ROCK1,ROCK2,RAMP1,ARHGEF12,PPP1R14A |
hsa00071 | Fatty acid degradation | 9/44 | −3.7701 | ACADL,ACAT1,ACAT2,ADH1A,ADH1B,ALDH2,ALDH3A2,ECI1,HADH,ACYP2,LDHA,LDHB,ACSS2,PFKM,PGM1 |
hsa03020 | RNA polymerase | 7/31 | −3.3221 | POLR2C,POLR2F,POLR2G,POLR2H,POLR2I,POLR3F,POLR3C,ADCY3,AK1,GUK1,NME3,PGM1,PRPS2,ENPP4,NME7,AK3,NUDT9,POLE4,NT5C3B,CTPS1 |
hsa05016 | Huntington’s disease | 20/193 | −3.1152 | COX5B,COX6C,COX7A1,COX7B,COX7C,HDAC2,NDUFA4,NDUFA8,NDUFB10,NDUFC1,POLR2C,POLR2F,POLR2G,POLR2H,POLR2I,SOD1,ATP5H,UQCRQ,NDUFA12,NDUFA4L2,UBE2G2,SNCAIP,PINK1,COX17,ATP6V1D,CAPN2,MAPK3,RYR3 |
hsa05200 | Pathways in cancer | 33/397 | −2.9576 | ADCY3,AGTR1,AR,COL4A1,E2F3,EDNRA,MECOM,FGF13,FOXO1,FZD2,GNA11,GSTP1,MSH6,HDAC2,HRAS,LAMA5,LAMC1,SMAD4,PDGFA,PDGFRB,MAPK3,PTEN,ROCK1,SLC2A1,TCEB1,ZBTB16,FZD3,CCDC6,ROCK2,GNB5,RALBP1,ARHGEF12,GNG12,PDGFC |
hsa05412 | Arrhythmogenic right ventricular cardiomyopathy (ARVC) | 10/74 | −2.6366 | ACTN1,CACNB3,CDH2,DAG1,GJA1,ITGA7,RYR2,SGCA,ITGA10,ITGA11 |
hsa00520 | Amino sugar and nucleotide sugar metabolism | 7/48 | −2.1749 | CYB5R3,GMDS,PGM1,PMM1,UAP1,UGDH,UGP2 |
Establishment of TFs-target genes regulatory network
TFs | Number | Target genes |
---|---|---|
Oct-1 | 10 | CCR7, CPVL, CSNK2A2, HBB, IL2RB, MGAM, NELL2, TRPC1, ZBTB16, ZNF462 |
HNF-4 | 10 | CCR7, CPVL, CSNK2A2, HBB, KLF15, MGAM, NELL2, NR2F6, PTGS2, ZNF462 |
Pax-4 | 8 | ADGRE3, CSNK2A2, FAM210B, NELL2, NR2F6, PDGFA, SYNC, ZBTB16 |
Evi-1 | 6 | CPVL, GBP5, HBB, NELL2, PTGS2, ZNF462 |
Nkx2–5 | 6 | CCR7, GBP5, MGAM, NELL2, TRPC1, ZBTB16 |