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Coexpression cluster:C1365: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0000468!4.61e-17!656;UBERON:0000467!3.10e-12!624;UBERON:0002204!4.26e-12!167;UBERON:0000480!5.73e-12!625;UBERON:0000062!1.26e-11!503;UBERON:0000923!1.30e-11!560;UBERON:0010316!1.30e-11!560;UBERON:0005291!1.30e-11!560;UBERON:0006598!1.30e-11!560;UBERON:0010317!1.30e-11!560;UBERON:0002532!1.30e-11!560;UBERON:0000926!1.45e-11!315;UBERON:0004120!1.45e-11!315;UBERON:0006603!1.45e-11!315;UBERON:0002050!1.92e-11!564;UBERON:0000922!3.53e-09!592;UBERON:0005423!3.73e-09!581;UBERON:0000479!3.45e-08!773;UBERON:0007524!4.28e-07!73;UBERON:0002384!7.61e-07!371
|ontology_enrichment_uberon=UBERON:0000468!4.61e-17!656;UBERON:0000467!3.10e-12!624;UBERON:0002204!4.26e-12!167;UBERON:0000480!5.73e-12!625;UBERON:0000062!1.26e-11!503;UBERON:0000923!1.30e-11!560;UBERON:0010316!1.30e-11!560;UBERON:0005291!1.30e-11!560;UBERON:0006598!1.30e-11!560;UBERON:0010317!1.30e-11!560;UBERON:0002532!1.30e-11!560;UBERON:0000926!1.45e-11!315;UBERON:0004120!1.45e-11!315;UBERON:0006603!1.45e-11!315;UBERON:0002050!1.92e-11!564;UBERON:0000922!3.53e-09!592;UBERON:0005423!3.73e-09!581;UBERON:0000479!3.45e-08!773;UBERON:0007524!4.28e-07!73;UBERON:0002384!7.61e-07!371
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|tfbs_overrepresentation_for_novel_motifs=0.44418,0.333388,0.436508,1.43205,1.01854,0.584466,0.662701,0.742622,0.736703,0.262261,0.553339,0.707204,1.18908,0.650887,0.391663,0.415981,0.889639,0.336106,0.664996,0.127969,0.436569,0.29639,0.576478,0.387783,0.483957,0.730467,0.202389,0.574247,0.396295,0.547818,0.530785,0.92701,0.816912,0.640661,0.35719,0.909936,0.35388,0.585658,0.329602,0.248856,0.355745,0.513952,1.10319,1.01199,1.41477,0.468392,0.66382,0.542147,1.05432,0.396429,0.745008,0.675919,0.149032,1.00488,1.15929,0.653901,0.400834,0.62023,0.547548,0.619193,0.968558,0.666252,0.737866,0.861462,0.684675,0.826413,1.24834,1.61834,0.916468,1.45553,0.500342,0.75612,0.146905,1.15727,0.218784,0.594475,0.562953,0.84426,0.913168,0.477584,0.240887,0.86037,0.684313,0.749276,1.10535,0.0481066,0.398737,0.181871,0.771626,1.71797,1.34233,1.07807,0.94406,0.30974,0.393853,0.32338,0.661488,0.987239,0.776336,0.166235,0.881389,0.938327,0.981588,0.893363,0.814675,0.548668,0.877269,0.647343,0.483695,0.376529,1.13818,0.978783,0.430775,0.563054,1.29401,0.352243,0.0577227,0.529546,0.824029,0.312699,1.14892,0.769145,0.581628,0.695878,1.40534,0.845034,0.656181,0.949126,1.1919,0.324369,1.07876,0.53374,1.20639,0.692462,1.35529,0.175219,0.524606,0.57483,1.31259,2.17352,1.7705,1.27501,0.657956,0.983666,0.816466,0.611524,0.799467,2.01411,1.27188,0.306342,0.424432,0.0926553,1.07915,1.32317,0.665754,1.48627,0.755083,0.986797,0.484017,1.15112,1.27379,1.06043,0.912368,0.457485,0.83286,0.683502,0.29379,0.661335,0.152397
}}
}}

Revision as of 14:50, 26 November 2012


Full id: C1365_Fibroblast_Adipocyte_Preadipocyte_Smooth_Chondrocyte_Mesenchymal_Pericytes



Phase1 CAGE Peaks

Hg19::chr12:57554837..57554851,+p@chr12:57554837..57554851
+
Hg19::chr12:57556203..57556225,+p@chr12:57556203..57556225
+
Hg19::chr12:57572239..57572259,+p@chr12:57572239..57572259
+
Hg19::chr12:57572685..57572712,+p@chr12:57572685..57572712
+
Hg19::chr12:57605894..57605910,+p@chr12:57605894..57605910
+


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

No GOStat results

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>

Cell Type
Ontology termp-valuen
fibroblast6.06e-1676
multi fate stem cell1.93e-09427
somatic stem cell1.73e-08433
stuff accumulating cell3.74e-0887
stem cell4.40e-08441
defensive cell5.81e-0848
phagocyte5.81e-0848
skin fibroblast5.16e-0723
connective tissue cell6.10e-07361
fat cell9.69e-0715
Uber Anatomy
Ontology termp-valuen
multi-cellular organism4.61e-17656
anatomical system3.10e-12624
musculoskeletal system4.26e-12167
anatomical group5.73e-12625
organ1.26e-11503
germ layer1.30e-11560
germ layer / neural crest1.30e-11560
embryonic tissue1.30e-11560
presumptive structure1.30e-11560
germ layer / neural crest derived structure1.30e-11560
epiblast (generic)1.30e-11560
mesoderm1.45e-11315
mesoderm-derived structure1.45e-11315
presumptive mesoderm1.45e-11315
embryonic structure1.92e-11564
embryo3.53e-09592
developing anatomical structure3.73e-09581
tissue3.45e-08773
dense mesenchyme tissue4.28e-0773
connective tissue7.61e-07371


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)

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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

This analysis result is provided for C0 - C305 clusters.

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