Coexpression cluster:C40
From FANTOM5_SSTAR
Full id: C40_eye_retina_Lens_pineal_tongue_retinoblastoma_small
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 |
|---|---|---|---|---|
| 4.83345641474546e-21 | 3.05957791053388e-18 | 12 | 29 | Phototransduction (KEGG):04744 |
| 1.35517186159513e-10 | 4.28911894194859e-08 | 6 | 17 | {CNGB1,17} (Static Module):NA |
| 8.55309257921433e-05 | 0.0180470253421422 | 3 | 18 | {OTX2,18} (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:0003008 | system process | 0 |
| GO:0007601 | visual perception | 9.28005666037585e-95 |
| GO:0050953 | sensory perception of light stimulus | 9.28005666037585e-95 |
| GO:0032501 | multicellular organismal process | 4.75541250480415e-58 |
| GO:0007600 | sensory perception | 4.1045935741495e-57 |
| GO:0050877 | neurological system process | 1.5411372358457e-52 |
| GO:0009584 | detection of visible light | 4.49089522501762e-29 |
| GO:0009583 | detection of light stimulus | 7.40022621362375e-29 |
| GO:0005212 | structural constituent of eye lens | 3.44889427763949e-28 |
| GO:0050962 | detection of light stimulus during sensory perception | 4.31549070751748e-27 |
| GO:0050908 | detection of light stimulus during visual perception | 4.31549070751748e-27 |
| GO:0009582 | detection of abiotic stimulus | 1.40047509303825e-26 |
| GO:0050906 | detection of stimulus during sensory perception | 1.97627418215132e-26 |
| GO:0009581 | detection of external stimulus | 9.00434831993419e-26 |
| GO:0007602 | phototransduction | 2.51838033293462e-25 |
| GO:0051606 | detection of stimulus | 4.74004200843173e-24 |
| GO:0009416 | response to light stimulus | 4.61006572285475e-22 |
| GO:0009314 | response to radiation | 1.95186369544272e-20 |
| GO:0009628 | response to abiotic stimulus | 6.49323376543073e-17 |
| GO:0007603 | phototransduction, visible light | 6.6106018274717e-09 |
| GO:0009605 | response to external stimulus | 5.51714854150995e-08 |
| GO:0005886 | plasma membrane | 4.31859602833272e-06 |
| GO:0009586 | rhodopsin mediated phototransduction | 6.16957634604802e-06 |
| GO:0016056 | rhodopsin mediated signaling | 6.16957634604802e-06 |
| GO:0044459 | plasma membrane part | 1.14421918953673e-05 |
| GO:0008048 | calcium sensitive guanylate cyclase activator activity | 1.41994535734861e-05 |
| GO:0001654 | eye development | 2.3472577783599e-05 |
| GO:0030250 | guanylate cyclase activator activity | 2.62999856641857e-05 |
| GO:0030249 | guanylate cyclase regulator activity | 4.28419357064365e-05 |
| GO:0001750 | photoreceptor outer segment | 4.28419357064365e-05 |
| GO:0042995 | cell projection | 6.04056214172142e-05 |
| GO:0005625 | soluble fraction | 6.08708280088107e-05 |
| GO:0031513 | nonmotile primary cilium | 9.29748915332394e-05 |
| GO:0046530 | photoreceptor cell differentiation | 0.000128570683930671 |
| GO:0005887 | integral to plasma membrane | 0.000159200861948719 |
| GO:0031226 | intrinsic to plasma membrane | 0.000180872506453625 |
| GO:0005929 | cilium | 0.000319265100671098 |
| GO:0005200 | structural constituent of cytoskeleton | 0.000319265100671098 |
| GO:0007423 | sensory organ development | 0.000329321645891407 |
| GO:0007154 | cell communication | 0.000560073589708165 |
| GO:0016020 | membrane | 0.000602841705538677 |
| GO:0009881 | photoreceptor activity | 0.000692789598533222 |
| GO:0017071 | intracellular cyclic nucleotide activated cation channel complex | 0.000702961623409981 |
| GO:0002088 | lens development in camera-type eye | 0.000702961623409981 |
| GO:0018298 | protein-chromophore linkage | 0.00103230567292462 |
| GO:0032502 | developmental process | 0.00103230567292462 |
| GO:0008092 | cytoskeletal protein binding | 0.00127877157210505 |
| GO:0007165 | signal transduction | 0.00127877157210505 |
| GO:0030551 | cyclic nucleotide binding | 0.00164279199645877 |
| GO:0047555 | 3',5'-cyclic-GMP phosphodiesterase activity | 0.00301066660739653 |
| GO:0007168 | receptor guanylyl cyclase signaling pathway | 0.00301066660739653 |
| GO:0003779 | actin binding | 0.00322284134000015 |
| GO:0043010 | camera-type eye development | 0.00385791840489341 |
| GO:0042461 | photoreceptor cell development | 0.00528233980031035 |
| GO:0044425 | membrane part | 0.00665436222718468 |
| GO:0000267 | cell fraction | 0.00674574472996517 |
| GO:0004745 | retinol dehydrogenase activity | 0.00800426326928108 |
| GO:0004114 | 3',5'-cyclic-nucleotide phosphodiesterase activity | 0.00811866182478278 |
| GO:0004112 | cyclic-nucleotide phosphodiesterase activity | 0.00897255159794482 |
| GO:0004385 | guanylate kinase activity | 0.00897255159794482 |
| GO:0019002 | GMP binding | 0.00897255159794482 |
| GO:0030553 | cGMP binding | 0.00897255159794482 |
| GO:0015629 | actin cytoskeleton | 0.00965296690744605 |
| GO:0007166 | cell surface receptor linked signal transduction | 0.00965296690744605 |
| GO:0032583 | regulation of gene-specific transcription | 0.0102455928279423 |
| GO:0030016 | myofibril | 0.0113847854074956 |
| GO:0005856 | cytoskeleton | 0.0113847854074956 |
| GO:0007030 | Golgi organization and biogenesis | 0.0134388765852486 |
| GO:0000187 | activation of MAPK activity | 0.0136307117177699 |
| GO:0045494 | photoreceptor cell maintenance | 0.0148157574683946 |
| GO:0006776 | vitamin A metabolic process | 0.0148157574683946 |
| GO:0044449 | contractile fiber part | 0.0151560436621496 |
| GO:0005515 | protein binding | 0.0154432675660726 |
| GO:0008081 | phosphoric diester hydrolase activity | 0.0175280685333669 |
| GO:0043292 | contractile fiber | 0.0175280685333669 |
| GO:0043406 | positive regulation of MAP kinase activity | 0.0188975687482529 |
| GO:0006775 | fat-soluble vitamin metabolic process | 0.019764354657535 |
| GO:0016776 | phosphotransferase activity, phosphate group as acceptor | 0.0215832859302441 |
| GO:0007186 | G-protein coupled receptor protein signaling pathway | 0.0215832859302441 |
| GO:0045211 | postsynaptic membrane | 0.0216829747528152 |
| GO:0022836 | gated channel activity | 0.0251334271244045 |
| GO:0044456 | synapse part | 0.0279736933200188 |
| GO:0022834 | ligand-gated channel activity | 0.0287896648415937 |
| GO:0015276 | ligand-gated ion channel activity | 0.0287896648415937 |
| GO:0005903 | brush border | 0.0287896648415937 |
| GO:0016021 | integral to membrane | 0.0287896648415937 |
| GO:0005249 | voltage-gated potassium channel activity | 0.0287896648415937 |
| GO:0031224 | intrinsic to membrane | 0.0297328191844264 |
| GO:0046534 | positive regulation of photoreceptor cell differentiation | 0.0297328191844264 |
| GO:0060040 | retinal bipolar neuron differentiation | 0.0297328191844264 |
| GO:0001918 | farnesylated protein binding | 0.0297328191844264 |
| GO:0031282 | regulation of guanylate cyclase activity | 0.0297328191844264 |
| GO:0009288 | flagellin-based flagellum | 0.0297328191844264 |
| GO:0050254 | rhodopsin kinase activity | 0.0297328191844264 |
| GO:0006649 | phospholipid transfer to membrane | 0.0297328191844264 |
| GO:0046532 | regulation of photoreceptor cell differentiation | 0.0297328191844264 |
| GO:0022838 | substrate specific channel activity | 0.0311651990342449 |
| GO:0007214 | gamma-aminobutyric acid signaling pathway | 0.0320366458460763 |
| GO:0048592 | eye morphogenesis | 0.0320366458460763 |
| GO:0022803 | passive transmembrane transporter activity | 0.0323387229660409 |
| GO:0015267 | channel activity | 0.0323387229660409 |
| GO:0019205 | nucleobase, nucleoside, nucleotide kinase activity | 0.034991268080682 |
| GO:0043405 | regulation of MAP kinase activity | 0.0368188627307908 |
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 |
|---|---|---|
| eye | 4.86e-20 | 21 |
| visual system | 4.86e-20 | 21 |
| retina | 9.07e-18 | 6 |
| photoreceptor array | 9.07e-18 | 6 |
| posterior segment of eyeball | 9.07e-18 | 6 |
| sense organ | 1.03e-17 | 24 |
| sensory system | 1.03e-17 | 24 |
| entire sense organ system | 1.03e-17 | 24 |
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 | 9.8926e-11 |
| MA0004.1 | 7.42032e-05 |
| MA0006.1 | 0.000180017 |
| MA0007.1 | 0.34058 |
| MA0009.1 | 0.0121072 |
| MA0014.1 | 0 |
| MA0017.1 | 0.412885 |
| MA0019.1 | 0.746106 |
| MA0024.1 | 0.000441712 |
| MA0025.1 | 0.391575 |
| MA0027.1 | 0.823941 |
| MA0028.1 | 1.0394e-06 |
| MA0029.1 | 0.963493 |
| MA0030.1 | 1.37042 |
| MA0031.1 | 0.918073 |
| MA0038.1 | 0.579443 |
| MA0040.1 | 2.44444 |
| MA0041.1 | 0.237759 |
| MA0042.1 | 0.902319 |
| MA0043.1 | 0.0121586 |
| MA0046.1 | 0.0695138 |
| MA0048.1 | 1.48509e-05 |
| MA0050.1 | 0.000311032 |
| MA0051.1 | 0.00626337 |
| MA0052.1 | 1.83001 |
| MA0055.1 | 0.686844 |
| MA0056.1 | 0 |
| MA0057.1 | 0.0646184 |
| MA0058.1 | 2.90659e-05 |
| MA0059.1 | 0.00828222 |
| MA0060.1 | 3.98308e-08 |
| MA0061.1 | 0.00418841 |
| MA0063.1 | 0 |
| MA0066.1 | 1.37264 |
| MA0067.1 | 0.193946 |
| MA0068.1 | 0.100297 |
| MA0069.1 | 0.219806 |
| MA0070.1 | 0.0252542 |
| MA0071.1 | 3.69469 |
| MA0072.1 | 3.84093 |
| MA0073.1 | 3.45849e-09 |
| MA0074.1 | 1.13096 |
| MA0076.1 | 3.09328e-06 |
| MA0077.1 | 0.0215432 |
| MA0078.1 | 0.624537 |
| MA0081.1 | 0.000363265 |
| MA0083.1 | 0.263065 |
| MA0084.1 | 0.449698 |
| MA0087.1 | 1.89481 |
| MA0088.1 | 0.117484 |
| MA0089.1 | 0 |
| MA0090.1 | 0.0552078 |
| MA0091.1 | 1.77079 |
| MA0092.1 | 2.10589 |
| MA0093.1 | 1.0983e-06 |
| MA0095.1 | 0 |
| MA0098.1 | 0 |
| MA0100.1 | 0.000748894 |
| MA0101.1 | 0.000129284 |
| MA0103.1 | 1.48189 |
| MA0105.1 | 0.00641015 |
| MA0106.1 | 0.0187931 |
| MA0107.1 | 0.0016282 |
| MA0108.2 | 1.58488 |
| MA0109.1 | 0 |
| MA0111.1 | 1.80389 |
| MA0113.1 | 0.329092 |
| MA0114.1 | 0.404243 |
| MA0115.1 | 0.121893 |
| MA0116.1 | 1.76652 |
| MA0117.1 | 0.328746 |
| MA0119.1 | 1.24403 |
| MA0122.1 | 0.794365 |
| MA0124.1 | 1.11799 |
| MA0125.1 | 1.02922 |
| MA0130.1 | 0 |
| MA0131.1 | 0.00965404 |
| MA0132.1 | 0 |
| MA0133.1 | 0 |
| MA0135.1 | 0.468297 |
| MA0136.1 | 0.000602123 |
| MA0139.1 | 0.0130063 |
| MA0140.1 | 0.937915 |
| MA0141.1 | 2.1747 |
| MA0142.1 | 0.145908 |
| MA0143.1 | 0.837569 |
| MA0144.1 | 0.129097 |
| MA0145.1 | 0.0891656 |
| MA0146.1 | 3.01686e-07 |
| MA0147.1 | 3.62935e-06 |
| MA0148.1 | 0.880184 |
| MA0149.1 | 0.00688097 |
| MA0062.2 | 1.01603e-07 |
| MA0035.2 | 0.787916 |
| MA0039.2 | 0 |
| MA0138.2 | 0.784662 |
| MA0002.2 | 0.449825 |
| MA0137.2 | 0.0500672 |
| MA0104.2 | 2.27184e-07 |
| MA0047.2 | 1.49726 |
| MA0112.2 | 1.37834 |
| MA0065.2 | 1.78212 |
| MA0150.1 | 0.573158 |
| MA0151.1 | 0 |
| MA0152.1 | 0.167133 |
| MA0153.1 | 0.486962 |
| MA0154.1 | 2.99544 |
| MA0155.1 | 0.040473 |
| MA0156.1 | 0.000191899 |
| MA0157.1 | 0.57972 |
| MA0158.1 | 0 |
| MA0159.1 | 0.546763 |
| MA0160.1 | 2.40899 |
| MA0161.1 | 0 |
| MA0162.1 | 0 |
| MA0163.1 | 2.17567e-06 |
| MA0164.1 | 2.25707 |
| MA0080.2 | 2.03597e-05 |
| MA0018.2 | 0.00973111 |
| MA0099.2 | 0.383474 |
| MA0079.2 | 0 |
| MA0102.2 | 0.0673613 |
| MA0258.1 | 3.67356 |
| MA0259.1 | 0.000933394 |
| 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
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
