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Coexpression cluster:C2869: Difference between revisions

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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C2869_optic_pineal_colon_breast_seminal_globus_kidney
|full_id=C2869_optic_pineal_colon_breast_seminal_globus_kidney
|id=C2869
|id=C2869

Revision as of 15:40, 12 September 2012


Full id: C2869_optic_pineal_colon_breast_seminal_globus_kidney



Phase1 CAGE Peaks

Hg19::chr6:76458921..76458934,+p3@MYO6
Hg19::chr6:76458948..76458964,+p1@MYO6
Hg19::chr6:76458969..76458980,+p4@MYO6
Hg19::chr6:76458990..76459011,+p2@MYO6


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
epithelial cell3.08e-08254
Uber Anatomy
Ontology termp-valuen
neural tube3.46e-2557
neural rod3.46e-2557
future spinal cord3.46e-2557
neural keel3.46e-2557
anatomical conduit4.72e-25241
organism subdivision1.35e-24365
central nervous system1.75e-2482
adult organism3.19e-24115
regional part of brain4.19e-2459
ectoderm-derived structure8.65e-24169
brain1.38e-2269
future brain1.38e-2269
regional part of nervous system2.64e-2294
nervous system2.64e-2294
anatomical cluster3.22e-22286
head4.63e-22123
ectoderm8.77e-22173
presumptive ectoderm8.77e-22173
anterior neural tube8.17e-2142
anterior region of body1.87e-20129
craniocervical region1.87e-20129
regional part of forebrain3.21e-2041
forebrain3.21e-2041
future forebrain3.21e-2041
multi-cellular organism4.45e-20659
tube1.20e-19194
neural plate8.09e-1986
presumptive neural plate8.09e-1986
cell layer4.16e-18312
anatomical group6.76e-18626
epithelium6.77e-18309
anatomical system7.35e-18625
multi-tissue structure9.07e-17347
organ1.07e-16511
neurectoderm2.64e-1690
gray matter6.52e-1634
brain grey matter6.52e-1634
telencephalon6.67e-1634
pre-chordal neural plate2.10e-1561
regional part of telencephalon2.16e-1533
cerebral hemisphere1.04e-1432
embryo1.76e-13612
organ part7.78e-13219
embryonic structure8.03e-12605
developing anatomical structure8.03e-12605
germ layer1.61e-11604
embryonic tissue1.61e-11604
presumptive structure1.61e-11604
epiblast (generic)1.61e-11604
regional part of cerebral cortex3.78e-1122
cerebral cortex4.13e-1125
pallium4.13e-1125
neocortex3.62e-1020
digestive system1.15e-07155
digestive tract1.15e-07155
primitive gut1.15e-07155
endoderm-derived structure2.83e-07169
endoderm2.83e-07169
presumptive endoderm2.83e-07169
immaterial anatomical entity3.98e-07126


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
CCNT2#90546.336201576962630.0006203100587215640.00513592533873644
E2F1#186944.907389214879320.001724022357361790.0106794288837786
EGR1#195844.988179094810140.001615011500076050.0101645285076801
ELF1#199744.258097958807540.003041525565781240.016125381418581
ETS1#211349.728760922202340.0001115955317418140.00154800448128347
HEY1#2346244.040111043105710.00375304636917980.0186587523087909
MYC#460945.22228187160940.001344309395272740.00889779637067554
SMARCB1#6598313.68953683586810.0006305783409379340.005182731671458
TAF1#687243.343046285745290.008005664898701650.0323281767913816
TBP#690843.706770687096390.005296377814784350.024499442049706
THAP1#55145431.36914460285131.03171810326891e-064.3256365711482e-05
ZBTB7A#5134147.35190930787590.000342223540015990.00347240690719226
ZEB1#6935416.88843201754391.22862303393937e-050.000305223979642231
ZNF263#1012748.221841637010680.0002187871180958320.00249889630651909



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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