Coexpression cluster:C25
From FANTOM5_SSTAR
Full id: C25_small_colon_temporal_duodenum_liver_Hepatocyte_gall
Phase1 CAGE Peaks
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
| p.value | FDR | nGenes | nPathway | Name |
|---|---|---|---|---|
| 0.00142070615699809 | 0.039100304233904 | 4 | 57 | Steroid hormone biosynthesis (KEGG):00140 |
| 7.31577314561641e-06 | 0.000704475932554023 | 6 | 55 | Starch and sucrose metabolism (KEGG):00500 |
| 6.64965018257481e-05 | 0.00350769047130821 | 5 | 50 | Glycerolipid metabolism (KEGG):00561 |
| 0.000686739167960443 | 0.0228792575431032 | 5 | 82 | Glycerophospholipid metabolism (KEGG):00564 |
| 0.00011796059375337 | 0.0049779370563922 | 4 | 30 | Linoleic acid metabolism (KEGG):00591 |
| 0.000217230282041052 | 0.00859417303324913 | 5 | 64 | Retinol metabolism (KEGG):00830 |
| 0.00100653159824771 | 0.0289606591677637 | 4 | 52 | Drug metabolism - other enzymes (KEGG):00983 |
| 1.23647832664343e-08 | 1.97099849742879e-06 | 31 | 1138 | Metabolic pathways (KEGG):01100 |
| 0.000353471044682319 | 0.0124303984046616 | 5 | 71 | PPAR signaling pathway (KEGG):03320 |
| 2.44183630259859e-07 | 3.09136475908982e-05 | 5 | 17 | Renin-angiotensin system (KEGG):04614 |
| 3.55293687812102e-05 | 0.00249889893761178 | 5 | 44 | Carbohydrate digestion and absorption (KEGG):04973 |
| 9.73119297336695e-11 | 3.07992257607064e-08 | 11 | 81 | Protein digestion and absorption (KEGG):04974 |
| 5.17189837676159e-12 | 3.27381167249009e-09 | 10 | 46 | Fat digestion and absorption (KEGG):04975 |
| 3.22650891760016e-05 | 0.00249889893761178 | 6 | 71 | Bile secretion (KEGG):04976 |
| 4.76090981245772e-05 | 0.00273968719207794 | 4 | 24 | Vitamin digestion and absorption (KEGG):04977 |
| 0.000935294303777572 | 0.0281924425852954 | 4 | 51 | Mineral absorption (KEGG):04978 |
| 4.76090981245772e-05 | 0.00273968719207794 | 4 | 24 | Triacylglyceride Synthesis (Wikipathways):WP325 |
| 0.000102917514876167 | 0.00480144688375243 | 4 | 29 | Statin Pathway (Wikipathways):WP430 |
| 0.000723459326667419 | 0.0228974876890238 | 3 | 21 | Urea cycle and metabolism of amino groups (Wikipathways):WP497 |
| 0.00010619313802928 | 0.00480144688375243 | 7 | 126 | Metabolism of carbohydrates (Reactome):REACT_474 |
| 7.79041315620562e-06 | 0.000704475932554023 | 12 | 289 | Metabolism of lipids and lipoproteins (Reactome):REACT_22258 |
| 1.24549668083968e-08 | 1.97099849742879e-06 | 18 | 401 | Transmembrane transport of small molecules (Reactome):REACT_15518 |
| 0.00025701754809309 | 0.0095701239966427 | 3 | 15 | {POR,15} (Static Module):NA |
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:0000267 | cell fraction | 1.12544389780385e-17 |
| GO:0016020 | membrane | 6.08255001418387e-15 |
| GO:0031224 | intrinsic to membrane | 3.21098138198736e-14 |
| GO:0016021 | integral to membrane | 6.76011191109321e-14 |
| GO:0006629 | lipid metabolic process | 6.8782604679198e-14 |
| GO:0044425 | membrane part | 1.6751637335342e-13 |
| GO:0005886 | plasma membrane | 8.69211312940586e-12 |
| GO:0045177 | apical part of cell | 3.99383959036168e-11 |
| GO:0016324 | apical plasma membrane | 2.07647900719527e-09 |
| GO:0005903 | brush border | 9.02630738144941e-09 |
| GO:0031226 | intrinsic to plasma membrane | 1.94041403178488e-07 |
| GO:0005624 | membrane fraction | 2.5344050515557e-07 |
| GO:0015293 | symporter activity | 4.59209216166811e-07 |
| GO:0044459 | plasma membrane part | 5.17413740066671e-07 |
| GO:0044464 | cell part | 6.89093349719874e-07 |
| GO:0005887 | integral to plasma membrane | 7.40895027274202e-07 |
| GO:0015926 | glucosidase activity | 1.80298354186049e-06 |
| GO:0005783 | endoplasmic reticulum | 2.92057414170324e-06 |
| GO:0044255 | cellular lipid metabolic process | 5.94708615287768e-06 |
| GO:0051234 | establishment of localization | 1.38907671724215e-05 |
| GO:0015291 | secondary active transmembrane transporter activity | 2.82006466616133e-05 |
| GO:0051179 | localization | 3.61266903134465e-05 |
| GO:0042995 | cell projection | 3.75039389601539e-05 |
| GO:0008237 | metallopeptidase activity | 4.08626220868809e-05 |
| GO:0005737 | cytoplasm | 4.11910099353472e-05 |
| GO:0007586 | digestion | 9.94388028075592e-05 |
| GO:0006810 | transport | 9.94388028075592e-05 |
| GO:0016411 | acylglycerol O-acyltransferase activity | 0.000103275872145059 |
| GO:0008238 | exopeptidase activity | 0.000118443653878755 |
| GO:0005902 | microvillus | 0.000160845549089421 |
| GO:0015294 | solute:cation symporter activity | 0.000292249778701444 |
| GO:0030249 | guanylate cyclase regulator activity | 0.000294010844532565 |
| GO:0008235 | metalloexopeptidase activity | 0.000316993069541305 |
| GO:0044444 | cytoplasmic part | 0.000411816499281356 |
| GO:0008289 | lipid binding | 0.000611507566414807 |
| GO:0015370 | solute:sodium symporter activity | 0.000611507566414807 |
| GO:0046943 | carboxylic acid transmembrane transporter activity | 0.00103680032280387 |
| GO:0005342 | organic acid transmembrane transporter activity | 0.00105736197964837 |
| GO:0004238 | meprin A activity | 0.00105736197964837 |
| GO:0016139 | glycoside catabolic process | 0.00105736197964837 |
| GO:0016137 | glycoside metabolic process | 0.00105736197964837 |
| GO:0008374 | O-acyltransferase activity | 0.00178366544572996 |
| GO:0005792 | microsome | 0.00199745697430033 |
| GO:0008202 | steroid metabolic process | 0.00223373593224197 |
| GO:0042598 | vesicular fraction | 0.00249218959611717 |
| GO:0015804 | neutral amino acid transport | 0.00253202394362272 |
| GO:0006814 | sodium ion transport | 0.00256292220182837 |
| GO:0008422 | beta-glucosidase activity | 0.00256292220182837 |
| GO:0003846 | 2-acylglycerol O-acyltransferase activity | 0.00256292220182837 |
| GO:0022892 | substrate-specific transporter activity | 0.00256450819043284 |
| GO:0005625 | soluble fraction | 0.00260563052466103 |
| GO:0015175 | neutral amino acid transmembrane transporter activity | 0.0031289541197748 |
| GO:0016810 | hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds | 0.00359274616047101 |
| GO:0005200 | structural constituent of cytoskeleton | 0.00384407150619422 |
| GO:0004553 | hydrolase activity, hydrolyzing O-glycosyl compounds | 0.00389490211706013 |
| GO:0022600 | digestive system process | 0.00403310177544757 |
| GO:0004046 | aminoacylase activity | 0.00409917202564802 |
| GO:0004144 | diacylglycerol O-acyltransferase activity | 0.00409917202564802 |
| GO:0005856 | cytoskeleton | 0.00437611574502685 |
| GO:0005351 | sugar:hydrogen ion symporter activity | 0.00437611574502685 |
| GO:0022804 | active transmembrane transporter activity | 0.00542423341095315 |
| GO:0051119 | sugar transmembrane transporter activity | 0.00542423341095315 |
| GO:0031402 | sodium ion binding | 0.00558515330898698 |
| GO:0015144 | carbohydrate transmembrane transporter activity | 0.00568215102593719 |
| GO:0001882 | nucleoside binding | 0.00568215102593719 |
| GO:0008451 | X-Pro aminopeptidase activity | 0.00568215102593719 |
| GO:0004558 | alpha-glucosidase activity | 0.00568215102593719 |
| GO:0005415 | nucleoside:sodium symporter activity | 0.00568215102593719 |
| GO:0046942 | carboxylic acid transport | 0.00568215102593719 |
| GO:0015849 | organic acid transport | 0.00588071313293244 |
| GO:0016798 | hydrolase activity, acting on glycosyl bonds | 0.00703310623217222 |
| GO:0015932 | nucleobase, nucleoside, nucleotide and nucleic acid transmembrane transporter activity | 0.00703310623217222 |
| GO:0030250 | guanylate cyclase activator activity | 0.00762250466649875 |
| GO:0015858 | nucleoside transport | 0.00762250466649875 |
| GO:0006082 | organic acid metabolic process | 0.00865013686024854 |
| GO:0015171 | amino acid transmembrane transporter activity | 0.00865013686024854 |
| GO:0008643 | carbohydrate transport | 0.00882832817713688 |
| GO:0007163 | establishment and/or maintenance of cell polarity | 0.00974178783088342 |
| GO:0008241 | peptidyl-dipeptidase activity | 0.00974178783088342 |
| GO:0004246 | peptidyl-dipeptidase A activity | 0.00974178783088342 |
| GO:0008533 | astacin activity | 0.00974178783088342 |
| GO:0022891 | substrate-specific transmembrane transporter activity | 0.0111144584954148 |
| GO:0006805 | xenobiotic metabolic process | 0.0113786688053664 |
| GO:0006865 | amino acid transport | 0.0116983112385633 |
| GO:0004180 | carboxypeptidase activity | 0.0135485309827009 |
| GO:0009410 | response to xenobiotic stimulus | 0.0144962100323886 |
| GO:0019752 | carboxylic acid metabolic process | 0.018453837413959 |
| GO:0055037 | recycling endosome | 0.0186727012962271 |
| GO:0031941 | filamentous actin | 0.0186727012962271 |
| GO:0050892 | intestinal absorption | 0.0186727012962271 |
| GO:0044432 | endoplasmic reticulum part | 0.0188587341479975 |
| GO:0004177 | aminopeptidase activity | 0.0198073182421266 |
| GO:0015837 | amine transport | 0.0205104007839666 |
| GO:0006071 | glycerol metabolic process | 0.0209493454403757 |
| GO:0006833 | water transport | 0.0209493454403757 |
| GO:0042044 | fluid transport | 0.0209493454403757 |
| GO:0030197 | extracellular matrix constituent, lubricant activity | 0.0209493454403757 |
| GO:0019751 | polyol metabolic process | 0.0217718960249966 |
| GO:0007588 | excretion | 0.0231396779978653 |
| GO:0016811 | hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides | 0.0237941495777721 |
| GO:0050832 | defense response to fungus | 0.0237941495777721 |
| GO:0016805 | dipeptidase activity | 0.0237941495777721 |
| GO:0017040 | ceramidase activity | 0.0237941495777721 |
| GO:0005789 | endoplasmic reticulum membrane | 0.0243013336180163 |
| GO:0015629 | actin cytoskeleton | 0.026143294918876 |
| GO:0048646 | anatomical structure formation | 0.0267661931012544 |
| GO:0042175 | nuclear envelope-endoplasmic reticulum network | 0.0268932073051246 |
| GO:0042594 | response to starvation | 0.0268932073051246 |
| GO:0016787 | hydrolase activity | 0.0270252603936914 |
| GO:0022857 | transmembrane transporter activity | 0.0270252603936914 |
| GO:0005975 | carbohydrate metabolic process | 0.0296492973479511 |
| GO:0045104 | intermediate filament cytoskeleton organization and biogenesis | 0.0302847790459729 |
| GO:0008206 | bile acid metabolic process | 0.0342728699539975 |
| GO:0045103 | intermediate filament-based process | 0.0342728699539975 |
| GO:0042221 | response to chemical stimulus | 0.0368937816340678 |
| GO:0005543 | phospholipid binding | 0.0389071207582673 |
| GO:0006641 | triacylglycerol metabolic process | 0.0389071207582673 |
| GO:0009743 | response to carbohydrate stimulus | 0.0389071207582673 |
| GO:0005001 | transmembrane receptor protein tyrosine phosphatase activity | 0.0389071207582673 |
| GO:0009620 | response to fungus | 0.0389071207582673 |
| GO:0019198 | transmembrane receptor protein phosphatase activity | 0.0389071207582673 |
| GO:0005337 | nucleoside transmembrane transporter activity | 0.0389071207582673 |
| GO:0005993 | trehalose catabolic process | 0.0389071207582673 |
| GO:0015361 | low affinity sodium:dicarboxylate symporter activity | 0.0389071207582673 |
| GO:0004925 | prolactin receptor activity | 0.0389071207582673 |
| GO:0042976 | activation of JAK protein | 0.0389071207582673 |
| GO:0050591 | quinine 3-monooxygenase activity | 0.0389071207582673 |
| GO:0010288 | response to lead ion | 0.0389071207582673 |
| GO:0015068 | glycine amidinotransferase activity | 0.0389071207582673 |
| GO:0001977 | renal regulation of blood volume | 0.0389071207582673 |
| GO:0009744 | response to sucrose stimulus | 0.0389071207582673 |
| GO:0002017 | aldosterone mediated regulation of blood volume | 0.0389071207582673 |
| GO:0005982 | starch metabolic process | 0.0389071207582673 |
| GO:0015067 | amidinotransferase activity | 0.0389071207582673 |
| GO:0046821 | extrachromosomal DNA | 0.0389071207582673 |
| GO:0016142 | O-glycoside catabolic process | 0.0389071207582673 |
| GO:0017090 | meprin A complex | 0.0389071207582673 |
| GO:0010045 | response to nickel ion | 0.0389071207582673 |
| GO:0030823 | regulation of cGMP metabolic process | 0.0389071207582673 |
| GO:0004230 | glutamyl aminopeptidase activity | 0.0389071207582673 |
| GO:0004575 | sucrose alpha-glucosidase activity | 0.0389071207582673 |
| GO:0016554 | cytidine to uridine editing | 0.0389071207582673 |
| GO:0003845 | 11-beta-hydroxysteroid dehydrogenase activity | 0.0389071207582673 |
| GO:0004587 | ornithine-oxo-acid transaminase activity | 0.0389071207582673 |
| GO:0046352 | disaccharide catabolic process | 0.0389071207582673 |
| GO:0035003 | subapical complex | 0.0389071207582673 |
| GO:0042977 | tyrosine phosphorylation of JAK2 protein | 0.0389071207582673 |
| GO:0033791 | 3alpha,7alpha,12alpha-trihydroxy-5beta-cholestanoyl-CoA 24-hydroxylase activity | 0.0389071207582673 |
| GO:0016140 | O-glycoside metabolic process | 0.0389071207582673 |
| GO:0000016 | lactase activity | 0.0389071207582673 |
| GO:0030827 | negative regulation of cGMP biosynthetic process | 0.0389071207582673 |
| GO:0004530 | deoxyribonuclease I activity | 0.0389071207582673 |
| GO:0019343 | cysteine biosynthetic process via cystathionine | 0.0389071207582673 |
| GO:0030824 | negative regulation of cGMP metabolic process | 0.0389071207582673 |
| GO:0004574 | oligo-1,6-glucosidase activity | 0.0389071207582673 |
| GO:0017042 | glycosylceramidase activity | 0.0389071207582673 |
| GO:0005847 | mRNA cleavage and polyadenylation specificity factor complex | 0.0389071207582673 |
| GO:0033780 | taurochenodeoxycholate 6alpha-hydroxylase activity | 0.0389071207582673 |
| GO:0007503 | fat body development | 0.0389071207582673 |
| GO:0005727 | extrachromosomal circular DNA | 0.0389071207582673 |
| GO:0005983 | starch catabolic process | 0.0389071207582673 |
| GO:0030826 | regulation of cGMP biosynthetic process | 0.0389071207582673 |
| GO:0001675 | acrosome formation | 0.0389071207582673 |
| GO:0042978 | ornithine decarboxylase activator activity | 0.0389071207582673 |
| GO:0004122 | cystathionine beta-synthase activity | 0.0389071207582673 |
| GO:0003958 | NADPH-hemoprotein reductase activity | 0.0389071207582673 |
| GO:0030251 | guanylate cyclase inhibitor activity | 0.0389071207582673 |
| GO:0044275 | cellular carbohydrate catabolic process | 0.0389071207582673 |
| GO:0043168 | anion binding | 0.0389071207582673 |
| GO:0031667 | response to nutrient levels | 0.0389071207582673 |
| GO:0031404 | chloride ion binding | 0.0389071207582673 |
| GO:0043167 | ion binding | 0.0415042400035987 |
| GO:0017124 | SH3 domain binding | 0.0415516937542475 |
| GO:0016052 | carbohydrate catabolic process | 0.0443907608101243 |
| GO:0031090 | organelle membrane | 0.0443907608101243 |
| GO:0005768 | endosome | 0.0448980493879185 |
| GO:0048503 | GPI anchor binding | 0.0488324132516499 |
| GO:0009991 | response to extracellular stimulus | 0.0488324132516499 |
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><br>uberon_data<br><br>
| Ontology term | p-value | n |
|---|---|---|
| adult organism | 5.63e-34 | 115 |
| multi-cellular organism | 1.02e-19 | 659 |
| anatomical system | 3.64e-17 | 625 |
| anatomical group | 9.10e-17 | 626 |
| embryo | 9.14e-16 | 612 |
| organ | 5.63e-14 | 511 |
| embryonic structure | 1.03e-13 | 605 |
| developing anatomical structure | 1.03e-13 | 605 |
| germ layer | 2.23e-13 | 604 |
| embryonic tissue | 2.23e-13 | 604 |
| presumptive structure | 2.23e-13 | 604 |
| epiblast (generic) | 2.23e-13 | 604 |
| anatomical conduit | 1.63e-11 | 241 |
| mesoderm | 1.26e-10 | 448 |
| mesoderm-derived structure | 1.26e-10 | 448 |
| presumptive mesoderm | 1.26e-10 | 448 |
| subdivision of digestive tract | 4.23e-10 | 129 |
| endodermal part of digestive tract | 4.23e-10 | 129 |
| anatomical cluster | 8.00e-10 | 286 |
| tube | 1.53e-09 | 194 |
| multi-tissue structure | 7.18e-09 | 347 |
| immaterial anatomical entity | 1.35e-07 | 126 |
| digestive system | 1.41e-07 | 155 |
| digestive tract | 1.41e-07 | 155 |
| primitive gut | 1.41e-07 | 155 |
| mixed endoderm/mesoderm-derived structure | 2.19e-07 | 130 |
| neural tube | 3.17e-07 | 57 |
| neural rod | 3.17e-07 | 57 |
| future spinal cord | 3.17e-07 | 57 |
| neural keel | 3.17e-07 | 57 |
| epithelium | 9.37e-07 | 309 |
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) |
|---|---|
|
{{{tfbs_overrepresentation_jaspar}}} |
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
No analysis results for this cluster
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
"{{{coexpression_dpi_cluster_scores_median}}}" is not a number.
