Coexpression cluster:C969: Difference between revisions
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Latest revision as of 11:34, 17 September 2013
Full id: C969_mature_insula_mesodermal_occipital_Preadipocyte_temporal_heart
Phase1 CAGE Peaks
| Hg19::chr10:118502070..118502084,- | p1@HSPA12A |
| Hg19::chr15:62682733..62682759,+ | p1@TLN2 |
| Hg19::chr21:35014829..35014912,+ | p1@ITSN1 |
| Hg19::chr2:54683419..54683442,+ | p2@SPTBN1 |
| Hg19::chr2:54683448..54683470,+ | p1@SPTBN1 |
| Hg19::chr2:54684327..54684399,+ | p4@SPTBN1 |
| Hg19::chr9:131314859..131314877,+ | p1@SPTAN1 |
| Hg19::chr9:87285539..87285560,+ | p21@NTRK2 |
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 |
|---|---|---|---|---|
| 3.79490086907914e-05 | 0.0120108612506355 | 2 | 46 | Interactions of the immunoglobulin superfamily (IgSF) member proteins (Reactome):REACT_23853 |
| 1.65551775624537e-06 | 0.00104794273970332 | 2 | 10 | {SPTAN1,10} (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:0005200 | structural constituent of cytoskeleton | 4.99147211879799e-05 |
| GO:0008091 | spectrin | 9.70308090475593e-05 |
| GO:0030864 | cortical actin cytoskeleton | 0.000136243055220067 |
| GO:0051693 | actin filament capping | 0.000136243055220067 |
| GO:0051016 | barbed-end actin filament capping | 0.000136243055220067 |
| GO:0030835 | negative regulation of actin filament depolymerization | 0.000136243055220067 |
| GO:0030834 | regulation of actin filament depolymerization | 0.000136243055220067 |
| GO:0030042 | actin filament depolymerization | 0.000136243055220067 |
| GO:0030863 | cortical cytoskeleton | 0.000143580142384078 |
| GO:0015629 | actin cytoskeleton | 0.000213216949059869 |
| GO:0008064 | regulation of actin polymerization and/or depolymerization | 0.000290516615129923 |
| GO:0044448 | cell cortex part | 0.000290516615129923 |
| GO:0051261 | protein depolymerization | 0.000290516615129923 |
| GO:0030832 | regulation of actin filament length | 0.000290516615129923 |
| GO:0032535 | regulation of cellular component size | 0.000290516615129923 |
| GO:0032956 | regulation of actin cytoskeleton organization and biogenesis | 0.000290516615129923 |
| GO:0051129 | negative regulation of cellular component organization and biogenesis | 0.000335265835546014 |
| GO:0051493 | regulation of cytoskeleton organization and biogenesis | 0.000343288446968344 |
| GO:0033043 | regulation of organelle organization and biogenesis | 0.000343288446968344 |
| GO:0003779 | actin binding | 0.000343288446968344 |
| GO:0008154 | actin polymerization and/or depolymerization | 0.000374299671112961 |
| GO:0005938 | cell cortex | 0.000393507614964763 |
| GO:0008092 | cytoskeletal protein binding | 0.000771815799853878 |
| GO:0051128 | regulation of cellular component organization and biogenesis | 0.000883182958994439 |
| GO:0051248 | negative regulation of protein metabolic process | 0.000917108549270258 |
| GO:0007010 | cytoskeleton organization and biogenesis | 0.00100030724883964 |
| GO:0005516 | calmodulin binding | 0.00156030768475826 |
| GO:0030036 | actin cytoskeleton organization and biogenesis | 0.00459280999558969 |
| GO:0030029 | actin filament-based process | 0.00488493878915314 |
| GO:0043121 | neurotrophin binding | 0.00488493878915314 |
| GO:0048488 | synaptic vesicle endocytosis | 0.00567241467434988 |
| GO:0016043 | cellular component organization and biogenesis | 0.00573061625175347 |
| GO:0005856 | cytoskeleton | 0.00662604076192401 |
| GO:0006996 | organelle organization and biogenesis | 0.00797412921710054 |
| GO:0007016 | cytoskeletal anchoring | 0.0091139899944362 |
| GO:0005886 | plasma membrane | 0.0091139899944362 |
| GO:0051246 | regulation of protein metabolic process | 0.0100232053533945 |
| GO:0030054 | cell junction | 0.0100807159878271 |
| GO:0009892 | negative regulation of metabolic process | 0.0101401678185353 |
| GO:0007043 | intercellular junction assembly | 0.0102515793004705 |
| GO:0045216 | intercellular junction assembly and maintenance | 0.0125492597196398 |
| GO:0048489 | synaptic vesicle transport | 0.0125492597196398 |
| GO:0007028 | cytoplasm organization and biogenesis | 0.0163360075800794 |
| GO:0044459 | plasma membrane part | 0.0196488111773652 |
| GO:0005624 | membrane fraction | 0.0211664538902833 |
| GO:0005925 | focal adhesion | 0.0215907385342878 |
| GO:0005515 | protein binding | 0.0215907385342878 |
| GO:0019717 | synaptosome | 0.0219321352358375 |
| GO:0005924 | cell-substrate adherens junction | 0.0226747890717908 |
| GO:0030055 | cell-matrix junction | 0.0233873930407654 |
| GO:0001726 | ruffle | 0.0246430376281777 |
| GO:0005912 | adherens junction | 0.0302912053126019 |
| GO:0000267 | cell fraction | 0.0302912053126019 |
| GO:0019538 | protein metabolic process | 0.0302912053126019 |
| GO:0044430 | cytoskeletal part | 0.0302912053126019 |
| GO:0043232 | intracellular non-membrane-bound organelle | 0.0302912053126019 |
| GO:0043228 | non-membrane-bound organelle | 0.0302912053126019 |
| GO:0065008 | regulation of biological quality | 0.0313083760599613 |
| GO:0031252 | leading edge | 0.0355917882053961 |
| GO:0016323 | basolateral plasma membrane | 0.0412782857834084 |
| GO:0048523 | negative regulation of cellular process | 0.0417652213505117 |
| GO:0019838 | growth factor binding | 0.0418142683574165 |
| GO:0048519 | negative regulation of biological process | 0.0435488653287554 |
| GO:0004714 | transmembrane receptor protein tyrosine kinase activity | 0.0495374653713563 |
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 |
|---|---|---|
| fibroblast | 3.84e-10 | 76 |
| mesodermal cell | 2.71e-07 | 121 |
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 | 4.69204 |
| MA0004.1 | 0.455723 |
| MA0006.1 | 0.300178 |
| MA0007.1 | 0.437331 |
| MA0009.1 | 0.918715 |
| MA0014.1 | 3.20776 |
| MA0017.1 | 0.337901 |
| MA0019.1 | 0.602411 |
| MA0024.1 | 0.813542 |
| MA0025.1 | 1.05265 |
| MA0027.1 | 2.5321 |
| MA0028.1 | 0.315574 |
| MA0029.1 | 0.832916 |
| MA0030.1 | 0.821423 |
| MA0031.1 | 0.756713 |
| MA0038.1 | 0.557409 |
| MA0040.1 | 0.838784 |
| MA0041.1 | 0.474018 |
| MA0042.1 | 0.442535 |
| MA0043.1 | 0.919032 |
| MA0046.1 | 0.90778 |
| MA0048.1 | 2.19172 |
| MA0050.1 | 0.443405 |
| MA0051.1 | 0.553205 |
| MA0052.1 | 0.842664 |
| MA0055.1 | 0.835832 |
| MA0056.1 | 0 |
| MA0057.1 | 1.05663 |
| MA0058.1 | 0.362328 |
| MA0059.1 | 0.361075 |
| MA0060.1 | 0.556724 |
| MA0061.1 | 0.165998 |
| MA0063.1 | 0 |
| MA0066.1 | 0.557833 |
| MA0067.1 | 1.23721 |
| MA0068.1 | 0.133123 |
| MA0069.1 | 0.903908 |
| MA0070.1 | 0.892666 |
| MA0071.1 | 0.518907 |
| MA0072.1 | 0.888148 |
| MA0073.1 | 5.03496 |
| MA0074.1 | 0.552456 |
| MA0076.1 | 0.377799 |
| MA0077.1 | 0.880402 |
| MA0078.1 | 0.652193 |
| MA0081.1 | 0.361233 |
| MA0083.1 | 0.926258 |
| MA0084.1 | 1.42483 |
| MA0087.1 | 0.885691 |
| MA0088.1 | 2.18672 |
| MA0089.1 | 0 |
| MA0090.1 | 0.391903 |
| MA0091.1 | 0.458301 |
| MA0092.1 | 0.421159 |
| MA0093.1 | 0.303084 |
| MA0095.1 | 0 |
| MA0098.1 | 0 |
| MA0100.1 | 0.571227 |
| MA0101.1 | 0.30624 |
| MA0103.1 | 0.291333 |
| MA0105.1 | 0.586268 |
| MA0106.1 | 0.59853 |
| MA0107.1 | 0.236528 |
| MA0108.2 | 0.753643 |
| MA0109.1 | 0 |
| MA0111.1 | 0.405141 |
| MA0113.1 | 0.614917 |
| MA0114.1 | 0.231781 |
| MA0115.1 | 1.1606 |
| MA0116.1 | 0.673701 |
| MA0117.1 | 0.956472 |
| MA0119.1 | 0.345493 |
| MA0122.1 | 0.982472 |
| MA0124.1 | 1.11898 |
| MA0125.1 | 1.0347 |
| MA0130.1 | 0 |
| MA0131.1 | 0.670358 |
| MA0132.1 | 0 |
| MA0133.1 | 0 |
| MA0135.1 | 0.949204 |
| MA0136.1 | 0.564434 |
| MA0139.1 | 0.155155 |
| MA0140.1 | 0.516266 |
| MA0141.1 | 0.359385 |
| MA0142.1 | 0.724856 |
| MA0143.1 | 0.615094 |
| MA0144.1 | 0.218541 |
| MA0145.1 | 0.220937 |
| MA0146.1 | 1.26525 |
| MA0147.1 | 0.243042 |
| MA0148.1 | 0.480298 |
| MA0149.1 | 0.506665 |
| MA0062.2 | 0.485915 |
| MA0035.2 | 0.515566 |
| MA0039.2 | 3.46158 |
| MA0138.2 | 0.653421 |
| MA0002.2 | 0.179788 |
| MA0137.2 | 0.321796 |
| MA0104.2 | 0.189646 |
| MA0047.2 | 0.586412 |
| MA0112.2 | 0.458158 |
| MA0065.2 | 0.844872 |
| MA0150.1 | 0.386144 |
| MA0151.1 | 0 |
| MA0152.1 | 0.52279 |
| MA0153.1 | 1.01778 |
| MA0154.1 | 0.274121 |
| MA0155.1 | 0.197713 |
| MA0156.1 | 0.323987 |
| MA0157.1 | 0.697424 |
| MA0158.1 | 0 |
| MA0159.1 | 0.682702 |
| MA0160.1 | 0.495355 |
| MA0161.1 | 0 |
| MA0162.1 | 1.70684 |
| MA0163.1 | 1.83367 |
| MA0164.1 | 0.627336 |
| MA0080.2 | 0.303167 |
| MA0018.2 | 0.599912 |
| MA0099.2 | 0.523145 |
| MA0079.2 | 16.0339 |
| MA0102.2 | 1.46209 |
| MA0258.1 | 0.603127 |
| MA0259.1 | 0.699589 |
| 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 | 5 | 3.06711825929958 | 0.0112973236497416 | 0.0414473314594218 |
| HEY1#23462 | 6 | 3.03008328232928 | 0.00400172346648327 | 0.0191889805838405 |
| TAF1#6872 | 7 | 2.92516550002713 | 0.00126532535791574 | 0.0084934324220941 |
| TAF7#6879 | 4 | 5.71653470246196 | 0.00306854155518016 | 0.0161774564099677 |
| ZNF263#10127 | 5 | 5.13865102313167 | 0.00108253124903356 | 0.0076401190105295 |
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.
