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Coexpression cluster:C2019: Difference between revisions

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|tf_chipseq_enrich=CTCF#10664;5:5.36025637307503:0.000225927829993709:0.00250325447026447!E2F6#1876;5:5.01715573169739:0.000314497859929779:0.00323349497865782!HEY1#23462;5:4.04011104310571:0.000928885220517799:0.00675146798981547!MAX#4149;5:6.45255550900712:8.93743970843928e-05:0.00130859002622976!MYC#4609;5:5.2222818716094:0.000257394484885061:0.00276877357162539!PAX5#5079;5:6.66956553117783:7.57493746384605e-05:0.00117185438273829!SPI1#6688;5:8.20432350852273:2.68916109982495e-05:0.000575873069724457!TAF1#6872;5:3.34304628574529:0.00239460009087031:0.0135586684136842!TAF7#6879;5:11.4330694049239:5.11611886715123e-06:0.000157617208957642!TBP#6908;5:3.70677068709639:0.00142875510672112:0.00920585813997454!TCF7L2#6934;5:10.7701765631373:6.89693748574565e-06:0.000200308468874802!TFAP2A#7020;5:16.518634373045:8.12390055913032e-07:3.54555808815299e-05!TFAP2C#7022;5:10.8092286098602:6.77323239348459e-06:0.000197594865347245!ZNF263#10127;5:8.22184163701068:2.6606316672286e-05:0.000572817379290225
|tf_chipseq_enrich=CTCF#10664;5:5.36025637307503:0.000225927829993709:0.00250325447026447!E2F6#1876;5:5.01715573169739:0.000314497859929779:0.00323349497865782!HEY1#23462;5:4.04011104310571:0.000928885220517799:0.00675146798981547!MAX#4149;5:6.45255550900712:8.93743970843928e-05:0.00130859002622976!MYC#4609;5:5.2222818716094:0.000257394484885061:0.00276877357162539!PAX5#5079;5:6.66956553117783:7.57493746384605e-05:0.00117185438273829!SPI1#6688;5:8.20432350852273:2.68916109982495e-05:0.000575873069724457!TAF1#6872;5:3.34304628574529:0.00239460009087031:0.0135586684136842!TAF7#6879;5:11.4330694049239:5.11611886715123e-06:0.000157617208957642!TBP#6908;5:3.70677068709639:0.00142875510672112:0.00920585813997454!TCF7L2#6934;5:10.7701765631373:6.89693748574565e-06:0.000200308468874802!TFAP2A#7020;5:16.518634373045:8.12390055913032e-07:3.54555808815299e-05!TFAP2C#7022;5:10.8092286098602:6.77323239348459e-06:0.000197594865347245!ZNF263#10127;5:8.22184163701068:2.6606316672286e-05:0.000572817379290225
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}}
}}

Revision as of 15:14, 26 November 2012


Full id: C2019_mature_sacrococcigeal_gastric_Adipocyte_Synoviocyte_Mesenchymal_Chondrocyte



Phase1 CAGE Peaks

Hg19::chr9:129884902..129884922,-p1@ANGPTL2
Hg19::chr9:129884924..129884937,-p3@ANGPTL2
Hg19::chr9:129884944..129884979,-p2@ANGPTL2
Hg19::chr9:129884994..129885007,-p4@ANGPTL2
Hg19::chr9:129885010..129885017,-p5@ANGPTL2


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
fibroblast3.64e-1376
non-terminally differentiated cell1.58e-12106
fat cell5.14e-1115
mesodermal cell7.41e-09121
muscle precursor cell2.22e-0858
myoblast2.22e-0858
multi-potent skeletal muscle stem cell2.22e-0858
contractile cell2.82e-0859
muscle cell4.73e-0855
electrically responsive cell4.75e-0861
electrically active cell4.75e-0861
Uber Anatomy
Ontology termp-valuen
anatomical cluster6.97e-12373
multi-cellular organism1.74e-11656
epithelium4.03e-11306
cell layer4.94e-11309
muscle tissue2.10e-1064
musculature2.10e-1064
musculature of body2.10e-1064
dense mesenchyme tissue2.39e-1073
splanchnic layer of lateral plate mesoderm3.85e-1083
adult organism4.46e-10114
somite6.47e-1071
presomitic mesoderm6.47e-1071
presumptive segmental plate6.47e-1071
dermomyotome6.47e-1071
trunk paraxial mesoderm6.47e-1071
epithelial vesicle6.73e-1078
paraxial mesoderm6.75e-1072
presumptive paraxial mesoderm6.75e-1072
skeletal muscle tissue8.72e-1062
striated muscle tissue8.72e-1062
myotome8.72e-1062
multi-tissue structure1.08e-09342
structure with developmental contribution from neural crest7.58e-09132
unilaminar epithelium1.12e-08148
anatomical system2.47e-08624
mesenchyme3.51e-08160
entire embryonic mesenchyme3.51e-08160
anatomical group3.75e-08625
trunk mesenchyme3.84e-08122
vasculature4.76e-0878
vascular system4.76e-0878
anatomical conduit5.86e-08240
primary circulatory organ1.12e-0727
adipose tissue1.18e-0714
multilaminar epithelium1.43e-0783
vessel3.44e-0768
epithelial tube open at both ends4.36e-0759
blood vessel4.36e-0759
blood vasculature4.36e-0759
vascular cord4.36e-0759
circulatory system5.68e-07112
epithelial tube6.27e-07117


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)

{{{tfbs_overrepresentation_jaspar}}}



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#promotersEnrichmentp-valueq-value
CTCF#1066455.360256373075030.0002259278299937090.00250325447026447
E2F6#187655.017155731697390.0003144978599297790.00323349497865782
HEY1#2346254.040111043105710.0009288852205177990.00675146798981547
MAX#414956.452555509007128.93743970843928e-050.00130859002622976
MYC#460955.22228187160940.0002573944848850610.00276877357162539
PAX5#507956.669565531177837.57493746384605e-050.00117185438273829
SPI1#668858.204323508522732.68916109982495e-050.000575873069724457
TAF1#687253.343046285745290.002394600090870310.0135586684136842
TAF7#6879511.43306940492395.11611886715123e-060.000157617208957642
TBP#690853.706770687096390.001428755106721120.00920585813997454
TCF7L2#6934510.77017656313736.89693748574565e-060.000200308468874802
TFAP2A#7020516.5186343730458.12390055913032e-073.54555808815299e-05
TFAP2C#7022510.80922860986026.77323239348459e-060.000197594865347245
ZNF263#1012758.221841637010682.6606316672286e-050.000572817379290225



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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