Coexpression cluster:C939
From FANTOM5_SSTAR
Full id: C939_neuroblastoma_argyrophil_small_cerebellum_retinoblastoma_pineal_medulloblastoma
Phase1 CAGE Peaks
| Hg19::chr2:182543057..182543068,- | p1@GQ904713 |
| Hg19::chr2:182543197..182543218,- | p4@NEUROD1 |
| Hg19::chr2:182543249..182543261,- | p5@NEUROD1 |
| Hg19::chr2:182543547..182543559,- | p9@NEUROD1 |
| Hg19::chr2:182545234..182545252,- | p1@NEUROD1 |
| Hg19::chr2:182545296..182545307,- | p3@NEUROD1 |
| Hg19::chr2:182545330..182545341,- | p2@CERKL |
| Hg19::chr2:182545363..182545372,- | p3@CERKL |
| Hg19::chr6:66194027..66194031,- | p@chr6:66194027..66194031 - |
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:0030902 | hindbrain development | 0.0428039440196433 |
| GO:0004143 | diacylglycerol kinase activity | 0.0428039440196433 |
| GO:0043010 | camera-type eye development | 0.0428039440196433 |
| GO:0007205 | protein kinase C activation | 0.0428039440196433 |
| GO:0001654 | eye development | 0.0428039440196433 |
| GO:0009952 | anterior/posterior pattern formation | 0.0428039440196433 |
| GO:0032147 | activation of protein kinase activity | 0.0428039440196433 |
| GO:0045165 | cell fate commitment | 0.0428039440196433 |
| GO:0007423 | sensory organ development | 0.0428039440196433 |
| GO:0003002 | regionalization | 0.0428039440196433 |
| GO:0007200 | G-protein signaling, coupled to IP3 second messenger (phospholipase C activating) | 0.0428039440196433 |
| GO:0007389 | pattern specification process | 0.0436576993985432 |
| GO:0048015 | phosphoinositide-mediated signaling | 0.0436576993985432 |
| GO:0007420 | brain development | 0.0436576993985432 |
| GO:0045944 | positive regulation of transcription from RNA polymerase II promoter | 0.0436576993985432 |
| GO:0045860 | positive regulation of protein kinase activity | 0.0436576993985432 |
| GO:0033674 | positive regulation of kinase activity | 0.0436576993985432 |
| GO:0051347 | positive regulation of transferase activity | 0.0436576993985432 |
| GO:0032501 | multicellular organismal process | 0.0496195203628137 |
| GO:0007601 | visual perception | 0.0496195203628137 |
| GO:0050953 | sensory perception of light stimulus | 0.0496195203628137 |
| GO:0045893 | positive regulation of transcription, DNA-dependent | 0.0496195203628137 |
| GO:0007417 | central nervous system development | 0.0496195203628137 |
| GO:0045859 | regulation of protein kinase activity | 0.0496195203628137 |
| GO:0043549 | regulation of kinase activity | 0.0496195203628137 |
| GO:0051338 | regulation of transferase activity | 0.0496195203628137 |
| GO:0043085 | positive regulation of catalytic activity | 0.0496195203628137 |
| GO:0019932 | second-messenger-mediated signaling | 0.0496195203628137 |
| GO:0003702 | RNA polymerase II transcription factor activity | 0.0496195203628137 |
| GO:0045941 | positive regulation of transcription | 0.0496195203628137 |
| GO:0045935 | positive regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process | 0.0497326468379995 |
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><br>
| Ontology term | p-value | n |
|---|---|---|
| neuron | 3.93e-07 | 6 |
| neuroblast | 3.93e-07 | 6 |
| electrically signaling cell | 3.93e-07 | 6 |
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 | 0.0913842 |
| MA0004.1 | 1.87712 |
| MA0006.1 | 1.34805 |
| MA0007.1 | 0.397529 |
| MA0009.1 | 0.870971 |
| MA0014.1 | 1.50001 |
| MA0017.1 | 0.301634 |
| MA0019.1 | 0.558663 |
| MA0024.1 | 0.766783 |
| MA0025.1 | 1.00397 |
| MA0027.1 | 2.48103 |
| MA0028.1 | 0.280275 |
| MA0029.1 | 0.785955 |
| MA0030.1 | 0.774581 |
| MA0031.1 | 0.710608 |
| MA0038.1 | 0.514558 |
| MA0040.1 | 0.791764 |
| MA0041.1 | 0.433167 |
| MA0042.1 | 0.402577 |
| MA0043.1 | 0.871285 |
| MA0046.1 | 0.860127 |
| MA0048.1 | 0.0764047 |
| MA0050.1 | 0.403421 |
| MA0051.1 | 0.510444 |
| MA0052.1 | 0.795605 |
| MA0055.1 | 0.0199484 |
| MA0056.1 | 0 |
| MA0057.1 | 1.9083 |
| MA0058.1 | 4.25461 |
| MA0059.1 | 5.28745 |
| MA0060.1 | 0.162248 |
| MA0061.1 | 0.139804 |
| MA0063.1 | 0 |
| MA0066.1 | 0.514973 |
| MA0067.1 | 1.18766 |
| MA0068.1 | 0.109867 |
| MA0069.1 | 0.856287 |
| MA0070.1 | 0.845142 |
| MA0071.1 | 0.47692 |
| MA0072.1 | 0.840664 |
| MA0073.1 | 3.05635 |
| MA0074.1 | 3.23534 |
| MA0076.1 | 0.339975 |
| MA0077.1 | 0.832987 |
| MA0078.1 | 0.607575 |
| MA0081.1 | 0.865814 |
| MA0083.1 | 0.878452 |
| MA0084.1 | 1.37471 |
| MA0087.1 | 0.838229 |
| MA0088.1 | 0.363555 |
| MA0089.1 | 0 |
| MA0090.1 | 0.353576 |
| MA0091.1 | 3.8401 |
| MA0092.1 | 0.381858 |
| MA0093.1 | 2.91169 |
| MA0095.1 | 0 |
| MA0098.1 | 0 |
| MA0100.1 | 1.30927 |
| MA0101.1 | 0.271368 |
| MA0103.1 | 0.257174 |
| MA0105.1 | 0.0643619 |
| MA0106.1 | 0.554855 |
| MA0107.1 | 0.205358 |
| MA0108.2 | 0.707575 |
| MA0109.1 | 0 |
| MA0111.1 | 0.366362 |
| MA0113.1 | 0.57094 |
| MA0114.1 | 0.200901 |
| MA0115.1 | 1.11137 |
| MA0116.1 | 0.599942 |
| MA0117.1 | 0.908433 |
| MA0119.1 | 0.308914 |
| MA0122.1 | 0.934245 |
| MA0124.1 | 1.06995 |
| MA0125.1 | 0.986127 |
| MA0130.1 | 0 |
| MA0131.1 | 0.625452 |
| MA0132.1 | 0 |
| MA0133.1 | 0 |
| MA0135.1 | 0.90122 |
| MA0136.1 | 0.521435 |
| MA0139.1 | 0.129876 |
| MA0140.1 | 0.474342 |
| MA0141.1 | 0.322254 |
| MA0142.1 | 0.679161 |
| MA0143.1 | 0.571113 |
| MA0144.1 | 0.1885 |
| MA0145.1 | 0.046841 |
| MA0146.1 | 0.0045741 |
| MA0147.1 | 3.33389 |
| MA0148.1 | 0.439278 |
| MA0149.1 | 0.464973 |
| MA0062.2 | 0.135498 |
| MA0035.2 | 0.473658 |
| MA0039.2 | 0.323611 |
| MA0138.2 | 0.608783 |
| MA0002.2 | 0.152495 |
| MA0137.2 | 0.28622 |
| MA0104.2 | 5.40426 |
| MA0047.2 | 0.542971 |
| MA0112.2 | 0.0433683 |
| MA0065.2 | 0.182082 |
| MA0150.1 | 0.34802 |
| MA0151.1 | 0 |
| MA0152.1 | 0.480711 |
| MA0153.1 | 0.969315 |
| MA0154.1 | 0.062786 |
| MA0155.1 | 0.156896 |
| MA0156.1 | 0.288314 |
| MA0157.1 | 0.652111 |
| MA0158.1 | 0 |
| MA0159.1 | 0.212043 |
| MA0160.1 | 1.15068 |
| MA0161.1 | 0 |
| MA0162.1 | 2.3084 |
| MA0163.1 | 0.101664 |
| MA0164.1 | 0.583138 |
| MA0080.2 | 0.268439 |
| MA0018.2 | 0.556211 |
| MA0099.2 | 0.481058 |
| MA0079.2 | 2.91533 |
| MA0102.2 | 1.41188 |
| MA0258.1 | 0.532421 |
| MA0259.1 | 0.218904 |
| 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 |
|---|---|---|---|---|
| ATF3#467 | 4 | 9.98363312267056 | 0.000412784327724188 | 0.00393203050010822 |
| NRF1#4899 | 4 | 5.42679086564929 | 0.00404669891206852 | 0.0193681860445225 |
| REST#5978 | 4 | 4.28890165161245 | 0.00945702594596283 | 0.0356705671122255 |
| SUZ12#23512 | 2 | 11.1368402024584 | 0.0130543531390231 | 0.0463121569172334 |
| TCF12#6938 | 4 | 4.72642884541619 | 0.00668035530260397 | 0.0284202870768119 |
| USF2#7392 | 4 | 5.77430994891982 | 0.00322324100537492 | 0.016701332970845 |
| ZNF263#10127 | 8 | 7.30830367734282 | 3.84008362723504e-07 | 1.8758395413695e-05 |
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.
