Coexpression cluster:C2899
From FANTOM5_SSTAR
Full id: C2899_epidermoid_oral_cervical_Small_large_placenta_mucinous
Phase1 CAGE Peaks
| Hg19::chr7:55086703..55086717,+ | p1@EGFR |
| Hg19::chr7:55086735..55086738,+ | p3@EGFR |
| Hg19::chr7:55086794..55086803,+ | p2@EGFR |
| Hg19::chr7:55087162..55087197,+ | p1@BC057802 |
Enriched pathways on this co-expression cluster<b>Summary:</b><br>Canonical pathway gene sets were compiled from Reactome, Wikipathways and KEGG. For the major signaling pathways, the transcriptionally-regulated genes (downstream targets) were obtained from Netpath. Combined, the canonical pathways and downstream targets totaled 489 human gene sets. The corresponding M. musculus gene sets were inferred by homology using the HomoloGene database. Enrichment for each of the canonical 489 pathways and gene sets included in the co-expression cluster was assessed by the hypergeometric probability. The resulting P values were also then adjusted by the Benjamini-Hochberg method for multiple comparisons.<br><b>Analyst: </b>Emmanuel Dimont<br><br>link to source dataset<br>data
No results for this coexpression
Enriched Gene Ontology terms on this co-expression cluster<b>Summary:</b> Results for GOStat analysis on co-expressed clusters. Each cluster with promoters mapping to at least two different genes was analysed with GOStat (PMID: 14962934) with default parameter. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br>data
| GO ID | GO name | FDR corrected p-value |
|---|---|---|
| GO:0004710 | MAP/ERK kinase kinase activity | 0.00323796067349582 |
| GO:0043006 | calcium-dependent phospholipase A2 activation | 0.00323796067349582 |
| GO:0032430 | positive regulation of phospholipase A2 activity | 0.00323796067349582 |
| GO:0032429 | regulation of phospholipase A2 activity | 0.00323796067349582 |
| GO:0005006 | epidermal growth factor receptor activity | 0.00323796067349582 |
| GO:0032431 | activation of phospholipase A2 | 0.00323796067349582 |
| GO:0030235 | nitric-oxide synthase regulator activity | 0.00323796067349582 |
| GO:0030128 | clathrin coat of endocytic vesicle | 0.00323796067349582 |
| GO:0030669 | clathrin-coated endocytic vesicle membrane | 0.00323796067349582 |
| GO:0030122 | AP-2 adaptor complex | 0.00323796067349582 |
| GO:0030666 | endocytic vesicle membrane | 0.00348703457145704 |
| GO:0050999 | regulation of nitric-oxide synthase activity | 0.00348703457145704 |
| GO:0045334 | clathrin-coated endocytic vesicle | 0.00348703457145704 |
| GO:0045429 | positive regulation of nitric oxide biosynthetic process | 0.00370052648399522 |
| GO:0051205 | protein insertion into membrane | 0.00388555280819498 |
| GO:0045428 | regulation of nitric oxide biosynthetic process | 0.00404745084186977 |
| GO:0051341 | regulation of oxidoreductase activity | 0.0044308935532048 |
| GO:0030132 | clathrin coat of coated pit | 0.0044308935532048 |
| GO:0051668 | localization within membrane | 0.0044308935532048 |
| GO:0007202 | phospholipase C activation | 0.00480471583809057 |
| GO:0030335 | positive regulation of cell migration | 0.00480471583809057 |
| GO:0050679 | positive regulation of epithelial cell proliferation | 0.00480471583809057 |
| GO:0004709 | MAP kinase kinase kinase activity | 0.00480471583809057 |
| GO:0051272 | positive regulation of cell motility | 0.00480471583809057 |
| GO:0040017 | positive regulation of locomotion | 0.00480471583809057 |
| GO:0046209 | nitric oxide metabolic process | 0.00480471583809057 |
| GO:0030125 | clathrin vesicle coat | 0.00480471583809057 |
| GO:0030139 | endocytic vesicle | 0.00480471583809057 |
| GO:0006809 | nitric oxide biosynthetic process | 0.00480471583809057 |
| GO:0042327 | positive regulation of phosphorylation | 0.00480471583809057 |
| GO:0030665 | clathrin coated vesicle membrane | 0.00480471583809057 |
| GO:0045937 | positive regulation of phosphate metabolic process | 0.00505931355233722 |
| GO:0050730 | regulation of peptidyl-tyrosine phosphorylation | 0.005494721142902 |
| GO:0050678 | regulation of epithelial cell proliferation | 0.00571404824734557 |
| GO:0007173 | epidermal growth factor receptor signaling pathway | 0.00593626123474233 |
| GO:0050673 | epithelial cell proliferation | 0.00593626123474233 |
| GO:0019722 | calcium-mediated signaling | 0.00647592134699164 |
| GO:0051015 | actin filament binding | 0.00664634032980721 |
| GO:0018108 | peptidyl-tyrosine phosphorylation | 0.00677028140821853 |
| GO:0005905 | coated pit | 0.00677028140821853 |
| GO:0018212 | peptidyl-tyrosine modification | 0.00677028140821853 |
| GO:0001932 | regulation of protein amino acid phosphorylation | 0.00677028140821853 |
| GO:0033238 | regulation of amine metabolic process | 0.00677028140821853 |
| GO:0006521 | regulation of amino acid metabolic process | 0.00677028140821853 |
| GO:0030120 | vesicle coat | 0.00717982584122986 |
| GO:0030662 | coated vesicle membrane | 0.00717982584122986 |
| GO:0030131 | clathrin adaptor complex | 0.00728541151536559 |
| GO:0030119 | AP-type membrane coat adaptor complex | 0.00728541151536559 |
| GO:0030334 | regulation of cell migration | 0.00792969960856119 |
| GO:0042325 | regulation of phosphorylation | 0.00809490168373955 |
| GO:0043406 | positive regulation of MAP kinase activity | 0.00809490168373955 |
| GO:0030118 | clathrin coat | 0.00809490168373955 |
| GO:0051174 | regulation of phosphorus metabolic process | 0.00809490168373955 |
| GO:0019220 | regulation of phosphate metabolic process | 0.00809490168373955 |
| GO:0051270 | regulation of cell motility | 0.00809490168373955 |
| GO:0009891 | positive regulation of biosynthetic process | 0.00809490168373955 |
| GO:0040012 | regulation of locomotion | 0.00815072859190327 |
| GO:0040011 | locomotion | 0.00815072859190327 |
| GO:0051345 | positive regulation of hydrolase activity | 0.00831076572863927 |
| GO:0004702 | receptor signaling protein serine/threonine kinase activity | 0.00831076572863927 |
| GO:0001503 | ossification | 0.00904573140532166 |
| GO:0007200 | G-protein signaling, coupled to IP3 second messenger (phospholipase C activating) | 0.00904573140532166 |
| GO:0031214 | biomineral formation | 0.00904573140532166 |
| GO:0043405 | regulation of MAP kinase activity | 0.00941032320734723 |
| GO:0046849 | bone remodeling | 0.00956443768171072 |
| GO:0048771 | tissue remodeling | 0.00994190742002941 |
| GO:0046982 | protein heterodimerization activity | 0.00994190742002941 |
| GO:0030659 | cytoplasmic vesicle membrane | 0.00994190742002941 |
| GO:0044433 | cytoplasmic vesicle part | 0.00994190742002941 |
| GO:0003690 | double-stranded DNA binding | 0.00994190742002941 |
| GO:0004714 | transmembrane receptor protein tyrosine kinase activity | 0.00994190742002941 |
| GO:0012506 | vesicle membrane | 0.0100160916833471 |
| GO:0030136 | clathrin-coated vesicle | 0.0100160916833471 |
| GO:0030117 | membrane coat | 0.0100160916833471 |
| GO:0048475 | coated membrane | 0.0100160916833471 |
| GO:0018193 | peptidyl-amino acid modification | 0.010310348460342 |
| GO:0019199 | transmembrane receptor protein kinase activity | 0.0106810650788044 |
| GO:0048015 | phosphoinositide-mediated signaling | 0.0107101776123323 |
| GO:0045860 | positive regulation of protein kinase activity | 0.0114694028675635 |
| GO:0033674 | positive regulation of kinase activity | 0.0114694028675635 |
| GO:0044271 | nitrogen compound biosynthetic process | 0.0114694028675635 |
| GO:0030135 | coated vesicle | 0.0114694028675635 |
| GO:0051347 | positive regulation of transferase activity | 0.0114694028675635 |
| GO:0043566 | structure-specific DNA binding | 0.0122579939782342 |
| GO:0005057 | receptor signaling protein activity | 0.0134851538637355 |
| GO:0005768 | endosome | 0.0145331723252254 |
| GO:0001501 | skeletal development | 0.0154539032144119 |
| GO:0007169 | transmembrane receptor protein tyrosine kinase signaling pathway | 0.0154539032144119 |
| GO:0009889 | regulation of biosynthetic process | 0.0157896059808673 |
| GO:0045786 | negative regulation of progression through cell cycle | 0.0161898033674791 |
| GO:0016477 | cell migration | 0.0164009747157506 |
| GO:0008284 | positive regulation of cell proliferation | 0.0164009747157506 |
| GO:0045859 | regulation of protein kinase activity | 0.0165031544003981 |
| GO:0043549 | regulation of kinase activity | 0.0166720528294891 |
| GO:0051338 | regulation of transferase activity | 0.0168373955021783 |
| GO:0043085 | positive regulation of catalytic activity | 0.0172691235919777 |
| GO:0019932 | second-messenger-mediated signaling | 0.0178922362989047 |
| GO:0016044 | membrane organization and biogenesis | 0.0187669557402615 |
| GO:0007167 | enzyme linked receptor protein signaling pathway | 0.0194912534659454 |
| GO:0009888 | tissue development | 0.0194912534659454 |
| GO:0004713 | protein-tyrosine kinase activity | 0.0194912534659454 |
| GO:0051336 | regulation of hydrolase activity | 0.0194912534659454 |
| GO:0016337 | cell-cell adhesion | 0.0215471564818085 |
| GO:0016023 | cytoplasmic membrane-bound vesicle | 0.0215471564818085 |
| GO:0031988 | membrane-bound vesicle | 0.0215471564818085 |
| GO:0000074 | regulation of progression through cell cycle | 0.0215471564818085 |
| GO:0051726 | regulation of cell cycle | 0.0215471564818085 |
| GO:0042802 | identical protein binding | 0.0215471564818085 |
| GO:0031325 | positive regulation of cellular metabolic process | 0.0215471564818085 |
| GO:0046983 | protein dimerization activity | 0.0215471564818085 |
| GO:0006928 | cell motility | 0.0221453381776589 |
| GO:0051674 | localization of cell | 0.0221453381776589 |
| GO:0009893 | positive regulation of metabolic process | 0.0224078340413604 |
| GO:0051246 | regulation of protein metabolic process | 0.0239327528040995 |
| GO:0031410 | cytoplasmic vesicle | 0.0239327528040995 |
| GO:0031982 | vesicle | 0.0241172243267275 |
| GO:0003779 | actin binding | 0.0242431927348918 |
| GO:0042127 | regulation of cell proliferation | 0.0257390433198227 |
| GO:0006520 | amino acid metabolic process | 0.0257948463737314 |
| GO:0005615 | extracellular space | 0.0284940539267632 |
| GO:0006519 | amino acid and derivative metabolic process | 0.0293289661004249 |
| GO:0008092 | cytoskeletal protein binding | 0.0318531090644711 |
| GO:0050790 | regulation of catalytic activity | 0.0318531090644711 |
| GO:0022402 | cell cycle process | 0.032640732595724 |
| GO:0009308 | amine metabolic process | 0.0329494878134935 |
| GO:0065009 | regulation of a molecular function | 0.0344868509827888 |
| GO:0006807 | nitrogen compound metabolic process | 0.0345722415217349 |
| GO:0004674 | protein serine/threonine kinase activity | 0.0353646017308371 |
| GO:0008283 | cell proliferation | 0.0373997008023936 |
| GO:0019752 | carboxylic acid metabolic process | 0.0394487422511399 |
| GO:0006082 | organic acid metabolic process | 0.0394487422511399 |
| GO:0007049 | cell cycle | 0.0411613485615605 |
| GO:0044421 | extracellular region part | 0.044308935532048 |
| GO:0045184 | establishment of protein localization | 0.0445582050890022 |
| GO:0048522 | positive regulation of cellular process | 0.0450968145975287 |
| GO:0022610 | biological adhesion | 0.0450968145975287 |
| GO:0007155 | cell adhesion | 0.0450968145975287 |
| GO:0008104 | protein localization | 0.0450968145975287 |
| GO:0033036 | macromolecule localization | 0.0471484345550758 |
| GO:0012505 | endomembrane system | 0.0475517653193386 |
| GO:0048518 | positive regulation of biological process | 0.0487760884432987 |
Enriched sample ontology terms on this co-expression cluster<b>Summary:</b>To summarize promoter activities (expression profile of a TSS region) across ~1000 samples, we performed enrichment analysis based on FANTOM5 Sample Ontology (FF ontology). The question here is “in which type of samples the promoter is more active”. To answer this question, we compared expressions (TPMs) in the samples associated with a sample ontology term and the rest of the samples by using the Mann-Whitney rank sum test. To summarize ontologies enriched in this co-expression cluster, we ran the same analysis on an averaged expression profile of all promoters that make up. <b>Analyst:</b> Hideya Kawaji <br><br>links to source dataset<br><br>cell_data<br>uberon_data<br>disease_data<br>
| Ontology term | p-value | n |
|---|---|---|
| epithelial cell | 1.45e-16 | 253 |
| endo-epithelial cell | 9.18e-12 | 42 |
| endodermal cell | 4.25e-11 | 58 |
| embryonic cell | 2.49e-09 | 250 |
| mesothelial cell | 1.24e-07 | 19 |
| fibroblast | 1.97e-07 | 76 |
| Ontology term | p-value | n |
|---|---|---|
| squamous cell carcinoma | 2.45e-07 | 14 |
Overrepresented TFBS (DNA) motifs on this co-expression cluster<b>Summary:</b>The values shown are the p-values for overrepresentation of the motif in this coexpression cluster. So a small p-value means a strong overrepresentation. <b>Analyst:</b> Michiel de Hoon <br><br>link to source data <br> Novel motifs <br>data <br><br> Jaspar motifs <br>data
Novel motifs
JASPAR motifs
| Motifs | -log10(p-value) |
|---|---|
| MA0003.1 | 2.92335 |
| MA0004.1 | 0.71247 |
| MA0006.1 | 0.532262 |
| MA0007.1 | 1.65296 |
| MA0009.1 | 1.20602 |
| MA0014.1 | 3.08565 |
| MA0017.1 | 0.577281 |
| MA0019.1 | 0.873355 |
| MA0024.1 | 1.09684 |
| MA0025.1 | 1.34373 |
| MA0027.1 | 2.83281 |
| MA0028.1 | 0.550763 |
| MA0029.1 | 1.11704 |
| MA0030.1 | 1.10506 |
| MA0031.1 | 1.03735 |
| MA0038.1 | 0.824639 |
| MA0040.1 | 1.12314 |
| MA0041.1 | 0.732902 |
| MA0042.1 | 0.697662 |
| MA0043.1 | 1.20635 |
| MA0046.1 | 1.19471 |
| MA0048.1 | 0.709734 |
| MA0050.1 | 0.69864 |
| MA0051.1 | 0.820063 |
| MA0052.1 | 1.12718 |
| MA0055.1 | 1.28887 |
| MA0056.1 | 0 |
| MA0057.1 | 0.248209 |
| MA0058.1 | 0.605914 |
| MA0059.1 | 0.604454 |
| MA0060.1 | 0.393285 |
| MA0061.1 | 2.54366 |
| MA0063.1 | 0 |
| MA0066.1 | 0.825101 |
| MA0067.1 | 1.53181 |
| MA0068.1 | 0.841508 |
| MA0069.1 | 1.19071 |
| MA0070.1 | 1.17908 |
| MA0071.1 | 0.782546 |
| MA0072.1 | 1.1744 |
| MA0073.1 | 0.100363 |
| MA0074.1 | 0.819248 |
| MA0076.1 | 0.623864 |
| MA0077.1 | 1.16637 |
| MA0078.1 | 0.926725 |
| MA0081.1 | 0.604638 |
| MA0083.1 | 1.21381 |
| MA0084.1 | 1.72172 |
| MA0087.1 | 1.17185 |
| MA0088.1 | 1.02755 |
| MA0089.1 | 0 |
| MA0090.1 | 0.640115 |
| MA0091.1 | 0.715356 |
| MA0092.1 | 0.673508 |
| MA0093.1 | 0.535768 |
| MA0095.1 | 0 |
| MA0098.1 | 0 |
| MA0100.1 | 0.83965 |
| MA0101.1 | 1.33363 |
| MA0103.1 | 0.521546 |
| MA0105.1 | 2.66951 |
| MA0106.1 | 3.33935 |
| MA0107.1 | 0.453492 |
| MA0108.2 | 1.03412 |
| MA0109.1 | 0 |
| MA0111.1 | 0.655276 |
| MA0113.1 | 2.05499 |
| MA0114.1 | 1.13665 |
| MA0115.1 | 1.45393 |
| MA0116.1 | 0.457606 |
| MA0117.1 | 1.24497 |
| MA0119.1 | 0.586221 |
| MA0122.1 | 1.27173 |
| MA0124.1 | 1.41151 |
| MA0125.1 | 1.32534 |
| MA0130.1 | 0 |
| MA0131.1 | 0.94608 |
| MA0132.1 | 0 |
| MA0133.1 | 0 |
| MA0135.1 | 1.23748 |
| MA0136.1 | 0.832277 |
| MA0139.1 | 0.344952 |
| MA0140.1 | 0.779643 |
| MA0141.1 | 0.602484 |
| MA0142.1 | 1.00381 |
| MA0143.1 | 0.887001 |
| MA0144.1 | 0.430413 |
| MA0145.1 | 0.569905 |
| MA0146.1 | 0.481 |
| MA0147.1 | 0.46175 |
| MA0148.1 | 0.739888 |
| MA0149.1 | 0.769072 |
| MA0062.2 | 0.353589 |
| MA0035.2 | 0.778873 |
| MA0039.2 | 0.483275 |
| MA0138.2 | 0.928035 |
| MA0002.2 | 0.379056 |
| MA0137.2 | 0.558189 |
| MA0104.2 | 0.392359 |
| MA0047.2 | 0.856092 |
| MA0112.2 | 0.187982 |
| MA0065.2 | 0.199162 |
| MA0150.1 | 0.633493 |
| MA0151.1 | 0 |
| MA0152.1 | 0.78681 |
| MA0153.1 | 1.30799 |
| MA0154.1 | 0.229241 |
| MA0155.1 | 0.533581 |
| MA0156.1 | 0.560797 |
| MA0157.1 | 0.97481 |
| MA0158.1 | 0 |
| MA0159.1 | 1.1691 |
| MA0160.1 | 0.756582 |
| MA0161.1 | 0 |
| MA0162.1 | 1.06783 |
| MA0163.1 | 0.918944 |
| MA0164.1 | 0.90014 |
| MA0080.2 | 0.535868 |
| MA0018.2 | 0.870662 |
| MA0099.2 | 0.7872 |
| MA0079.2 | 6.45898 |
| MA0102.2 | 1.75932 |
| MA0258.1 | 0.418966 |
| MA0259.1 | 0.471671 |
| MA0442.1 | 0 |
ENCODE TF ChIP-seq peak enrichment analysis<b>Summary:</b> For each TF and each co-expression cluster, the number of promoters with ENCODE TF ChIP signal was compared with the rest of promoters from the robust set using Fisher's exact test. Clusters with significant ChIP enrichment (q <= 0.05) after Benjamini-Hochberg correction were retained. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br><br>data
(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)
| TF | #promoters | Enrichment | p-value | q-value |
|---|---|---|---|---|
| E2F1#1869 | 4 | 4.90738921487932 | 0.00172402235736179 | 0.0106806958702401 |
| TFAP2A#7020 | 3 | 12.3889757797837 | 0.00084694130358843 | 0.00638286208727609 |
| TFAP2C#7022 | 3 | 8.10692145739517 | 0.00294701173986644 | 0.0157216610869853 |
| ZNF263#10127 | 4 | 8.22184163701068 | 0.000218787118095832 | 0.00249998991540597 |
Relative expression of the co-expression cluster<b>Summary:</b>Co-expression clusters are compared against FANTOM5 samples to obtain relative expression. <br><b>Analyst:</b>NA<br><br>link to data source<br> data
This analysis result is provided for C0 - C305 clusters.
