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Coexpression cluster:C1192: Difference between revisions

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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C1192_extraskeletal_Cardiac_Lens_cholangiocellular_pineal_Fibroblast_rectum
|full_id=C1192_extraskeletal_Cardiac_Lens_cholangiocellular_pineal_Fibroblast_rectum
|id=C1192
|id=C1192

Revision as of 13:40, 12 September 2012


Full id: C1192_extraskeletal_Cardiac_Lens_cholangiocellular_pineal_Fibroblast_rectum



Phase1 CAGE Peaks

Hg19::chr13:93879041..93879078,+p1@GPC6
Hg19::chr13:93879085..93879136,+p2@GPC6
Hg19::chr13:93879137..93879148,+p10@GPC6
Hg19::chr13:93879165..93879189,+p3@GPC6
Hg19::chr13:93879196..93879223,+p4@GPC6
Hg19::chr13:93879225..93879248,+p9@GPC6
Hg19::chr13:93879313..93879326,+p7@GPC6


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
non-terminally differentiated cell1.04e-26180
fibroblast1.63e-1275
electrically responsive cell1.09e-0960
electrically active cell1.09e-0960
muscle precursor cell8.53e-0957
myoblast8.53e-0957
multi-potent skeletal muscle stem cell8.53e-0957
muscle cell1.66e-0854
contractile cell3.63e-0859
neural cell3.70e-0725
Uber Anatomy
Ontology termp-valuen
organism subdivision2.12e-26365
multi-tissue structure4.28e-20347
cell layer4.54e-16312
epithelium1.01e-15309
trunk1.27e-12216
multi-cellular organism1.08e-11659
trunk mesenchyme1.10e-11143
regional part of nervous system1.22e-1194
nervous system1.22e-1194
tube1.89e-10194
central nervous system4.19e-1082
anatomical cluster7.91e-10286
ectoderm1.39e-09173
presumptive ectoderm1.39e-09173
neurectoderm1.94e-0990
anatomical conduit3.74e-09241
embryo4.63e-09612
ectoderm-derived structure8.14e-09169
muscle tissue1.13e-0863
musculature1.13e-0863
musculature of body1.13e-0863
skeletal muscle tissue1.40e-0861
striated muscle tissue1.40e-0861
myotome1.40e-0861
neural plate1.47e-0886
presumptive neural plate1.47e-0886
embryonic structure3.60e-08605
developing anatomical structure3.60e-08605
germ layer6.55e-08604
embryonic tissue6.55e-08604
presumptive structure6.55e-08604
epiblast (generic)6.55e-08604
head6.87e-08123
dermomyotome8.26e-0870
somite1.11e-0783
paraxial mesoderm1.11e-0783
presomitic mesoderm1.11e-0783
presumptive segmental plate1.11e-0783
trunk paraxial mesoderm1.11e-0783
presumptive paraxial mesoderm1.11e-0783
mesenchyme1.18e-07238
entire embryonic mesenchyme1.18e-07238
brain1.71e-0769
future brain1.71e-0769
anterior region of body1.97e-07129
craniocervical region1.97e-07129
abdominal segment of trunk2.45e-0761
abdomen2.45e-0761
subdivision of trunk3.42e-07113
pre-chordal neural plate5.52e-0761
anatomical system8.41e-07625
anatomical group8.96e-07626


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
BHLHE40#8553744.87181354697742.71655591272133e-123.64671443404503e-10
EP300#203376.77394172622321.52695018318475e-065.85867561284469e-05
HEY1#2346274.040111043105715.68979821988558e-050.000950018922920273
JUND#372776.994663941871031.21993360047445e-064.92495729802671e-05
MAX#414976.452555509007122.14589603858566e-067.76829242197047e-05
POLR2A#543072.147453176558070.004747636447610280.0223370755451829
RAD21#5885710.35503389545637.82487927673307e-084.69668141829152e-06
REST#597879.650028716128021.28195528172884e-077.31618183980753e-06
RFX5#5993712.04791082719512.7106444306642e-081.86003281007975e-06
SETDB1#9869740.32002617801055.74662948954468e-127.45555574234232e-10
SP1#666775.69838137814095.12280185510121e-060.000157220188934739
TAF1#687273.343046285745290.0002142336319622450.00246576441354474
TBP#690873.706770687096390.0001039672097505110.00145085935584362
TRIM28#10155718.59052504526251.300439693691e-091.17386880872424e-07
YY1#752874.911170749853861.45048003565243e-050.000345386877436169
ZNF263#1012778.221841637010683.93423095812578e-071.90844006983603e-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.