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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C3650_aorta_cervix_Wilms_small_bladder_choriocarcinoma_Preadipocyte
|full_id=C3650_aorta_cervix_Wilms_small_bladder_choriocarcinoma_Preadipocyte
|id=C3650
|id=C3650

Revision as of 16:36, 12 September 2012


Full id: C3650_aorta_cervix_Wilms_small_bladder_choriocarcinoma_Preadipocyte



Phase1 CAGE Peaks

Hg19::chr17:47653178..47653241,+p1@NXPH3
Hg19::chr17:47653277..47653291,+p4@NXPH3
Hg19::chr17:47653471..47653492,+p2@NXPH3


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><br>uberon_data<br><br>

Uber Anatomy
Ontology termp-valuen
adult organism3.54e-35115
neural tube2.82e-1757
neural rod2.82e-1757
future spinal cord2.82e-1757
neural keel2.82e-1757
anterior neural tube4.27e-1642
central nervous system5.69e-1682
regional part of forebrain1.30e-1541
forebrain1.30e-1541
future forebrain1.30e-1541
brain6.65e-1569
future brain6.65e-1569
regional part of brain8.58e-1559
regional part of nervous system4.88e-1394
nervous system4.88e-1394
telencephalon7.07e-1334
gray matter2.23e-1234
brain grey matter2.23e-1234
regional part of telencephalon3.09e-1233
cerebral hemisphere3.75e-1232
regional part of cerebral cortex4.23e-1222
neocortex2.14e-1120
cerebral cortex5.98e-1125
pallium5.98e-1125
neural plate3.15e-1086
presumptive neural plate3.15e-1086
neurectoderm3.15e-1090
anatomical conduit2.71e-09241
tube3.96e-09194
anterior region of body1.10e-08129
craniocervical region1.10e-08129
head1.15e-08123
pre-chordal neural plate1.85e-0861
anatomical cluster5.48e-08286
ectoderm6.04e-08173
presumptive ectoderm6.04e-08173
organism subdivision6.24e-08365
ectoderm-derived structure7.82e-08169
multi-cellular organism8.02e-08659


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#90536.336201576962630.003930750035764890.0189846283289516
CTCF#1066435.360256373075030.0064925092527670.0279168007678263
CTCFL#140690319.74647435897440.0001298372005551160.00171581265200251
E2F1#186934.907389214879320.008460985347239390.0324933571862598
E2F6#187635.017155731697390.00791769806886330.0321732343247223
RAD21#5885310.35503389545630.0009004912073565420.00663419873060876
SMC3#9126315.04493284493280.0002935825420371870.00308776103804851
ZBTB7A#5134137.35190930787590.002516255860282270.0140015581966018



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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