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Coexpression cluster:C1492: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0004923!5.13e-12!66;UBERON:0000481!1.96e-10!342;UBERON:0000468!4.18e-10!656;UBERON:0007023!9.50e-10!114;UBERON:0003102!7.03e-09!99;UBERON:0007524!2.07e-08!73;UBERON:0000467!3.23e-08!624;UBERON:0010314!3.47e-08!132;UBERON:0000064!4.23e-08!218;UBERON:0000480!5.06e-08!625;UBERON:0003077!5.35e-08!72;UBERON:0007285!5.35e-08!72;UBERON:0002329!5.73e-08!71;UBERON:0003059!5.73e-08!71;UBERON:0007282!5.73e-08!71;UBERON:0004290!5.73e-08!71;UBERON:0009618!5.73e-08!71;UBERON:0007503!8.05e-08!78;UBERON:0005256!9.94e-08!122;UBERON:0005631!1.33e-07!14;UBERON:0000158!1.33e-07!14;UBERON:0002385!1.67e-07!64;UBERON:0001015!1.67e-07!64;UBERON:0000383!1.67e-07!64;UBERON:0000477!1.85e-07!373;UBERON:0000119!3.09e-07!309;UBERON:0000475!3.18e-07!264;UBERON:0001134!3.58e-07!62;UBERON:0002036!3.58e-07!62;UBERON:0003082!3.58e-07!62;UBERON:0000486!3.61e-07!83;UBERON:0002199!4.44e-07!46;UBERON:0002416!4.44e-07!46;UBERON:0000483!7.17e-07!306;UBERON:0001013!7.46e-07!14
|ontology_enrichment_uberon=UBERON:0004923!5.13e-12!66;UBERON:0000481!1.96e-10!342;UBERON:0000468!4.18e-10!656;UBERON:0007023!9.50e-10!114;UBERON:0003102!7.03e-09!99;UBERON:0007524!2.07e-08!73;UBERON:0000467!3.23e-08!624;UBERON:0010314!3.47e-08!132;UBERON:0000064!4.23e-08!218;UBERON:0000480!5.06e-08!625;UBERON:0003077!5.35e-08!72;UBERON:0007285!5.35e-08!72;UBERON:0002329!5.73e-08!71;UBERON:0003059!5.73e-08!71;UBERON:0007282!5.73e-08!71;UBERON:0004290!5.73e-08!71;UBERON:0009618!5.73e-08!71;UBERON:0007503!8.05e-08!78;UBERON:0005256!9.94e-08!122;UBERON:0005631!1.33e-07!14;UBERON:0000158!1.33e-07!14;UBERON:0002385!1.67e-07!64;UBERON:0001015!1.67e-07!64;UBERON:0000383!1.67e-07!64;UBERON:0000477!1.85e-07!373;UBERON:0000119!3.09e-07!309;UBERON:0000475!3.18e-07!264;UBERON:0001134!3.58e-07!62;UBERON:0002036!3.58e-07!62;UBERON:0003082!3.58e-07!62;UBERON:0000486!3.61e-07!83;UBERON:0002199!4.44e-07!46;UBERON:0002416!4.44e-07!46;UBERON:0000483!7.17e-07!306;UBERON:0001013!7.46e-07!14
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|tfbs_overrepresentation_for_novel_motifs=0.44418,0.946942,1.11302,0.58616,0.393082,0.584466,0.662701,0.269608,0.267027,0.262261,0.553339,0.707204,0.635275,0.650887,0.391663,1.06849,0.889639,0.336106,0.236034,0.402028,0.436569,0.29639,0.576478,0.387783,0.483957,0.730467,0.202389,0.574247,0.396295,0.186644,0.530785,0.92701,0.816912,0.225641,0.35719,0.577216,0.35388,0.585658,1.5795,0.248856,0.936389,0.513952,0.0979105,0.390088,0.154075,0.468392,0.66382,0.542147,0.0909286,0.396429,0.745008,0.675919,0.149032,1.00488,1.15929,0.653901,0.400834,0.62023,0.186533,0.619193,0.968558,0.666252,0.267534,0.861462,0.684675,0.826413,1.24834,1.61834,0.916468,1.45553,0.500342,0.275507,0.146905,1.15727,0.624519,0.206105,0.192925,0.84426,0.913168,0.477584,0.676305,0.86037,0.684313,0.272514,1.10535,0.181326,0.398737,0.536262,0.771626,1.71797,1.34233,1.07807,0.94406,0.83374,0.393853,0.32338,1.23175,0.987239,0.776336,0.166235,0.330999,0.938327,0.981588,0.893363,0.814675,0.548668,0.877269,0.647343,0.483695,0.376529,0.44815,0.978783,0.430775,0.563054,1.29401,0.928633,0.210279,0.529546,0.824029,0.312699,1.14892,0.769145,0.581628,0.695878,1.40534,0.845034,0.656181,0.949126,1.1919,0.324369,1.07876,0.53374,1.20639,0.692462,1.35529,0.520084,0.524606,0.57483,1.31259,2.17352,1.7705,1.27501,0.657956,0.983666,0.816466,0.611524,0.799467,2.01411,0.510514,0.306342,0.136746,0.0926553,1.07915,0.258882,0.665754,1.48627,0.755083,0.986797,0.484017,1.15112,1.27379,1.06043,0.912368,0.457485,0.83286,0.683502,0.79772,0.661335,0.307168
}}
}}

Revision as of 14:55, 26 November 2012


Full id: C1492_chorionic_amniotic_Smooth_basal_spindle_placenta_mesenchymal



Phase1 CAGE Peaks

Hg19::chr22:33197683..33197698,+p1@TIMP3
Hg19::chr22:33253227..33253256,+p@chr22:33253227..33253256
+
Hg19::chr22:33255260..33255310,-p2@CU676956
Hg19::chr22:33255345..33255482,-p1@CU676956
Hg19::chr22:33256226..33256238,-p4@ENST00000327661
Hg19::chr22:33256911..33256925,+p3@TIMP3


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 IDGO nameFDR corrected p-value
GO:0008191metalloendopeptidase inhibitor activity0.00900741787354292
GO:0007169transmembrane receptor protein tyrosine kinase signaling pathway0.0227077761517889
GO:0050953sensory perception of light stimulus0.0227077761517889
GO:0007601visual perception0.0227077761517889
GO:0004866endopeptidase inhibitor activity0.0227077761517889
GO:0030414protease inhibitor activity0.0227077761517889
GO:0007167enzyme linked receptor protein signaling pathway0.0227077761517889
GO:0004857enzyme inhibitor activity0.0247851171553044
GO:0005578proteinaceous extracellular matrix0.0247851171553044
GO:0044421extracellular region part0.0457596095179988
GO:0007600sensory perception0.0457596095179988



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
fibroblast1.10e-1176
preadipocyte5.67e-0812
smooth muscle cell5.96e-0743
smooth muscle myoblast5.96e-0743
muscle cell6.08e-0755
Uber Anatomy
Ontology termp-valuen
organ component layer5.13e-1266
multi-tissue structure1.96e-10342
multi-cellular organism4.18e-10656
adult organism9.50e-10114
surface structure7.03e-0999
dense mesenchyme tissue2.07e-0873
anatomical system3.23e-08624
structure with developmental contribution from neural crest3.47e-08132
organ part4.23e-08218
anatomical group5.06e-08625
paraxial mesoderm5.35e-0872
presumptive paraxial mesoderm5.35e-0872
somite5.73e-0871
presomitic mesoderm5.73e-0871
presumptive segmental plate5.73e-0871
dermomyotome5.73e-0871
trunk paraxial mesoderm5.73e-0871
epithelial vesicle8.05e-0878
trunk mesenchyme9.94e-08122
extraembryonic membrane1.33e-0714
membranous layer1.33e-0714
muscle tissue1.67e-0764
musculature1.67e-0764
musculature of body1.67e-0764
anatomical cluster1.85e-07373
cell layer3.09e-07309
organism subdivision3.18e-07264
skeletal muscle tissue3.58e-0762
striated muscle tissue3.58e-0762
myotome3.58e-0762
multilaminar epithelium3.61e-0783
integument4.44e-0746
integumental system4.44e-0746
epithelium7.17e-07306
adipose tissue7.46e-0714


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.