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Coexpression cluster:C3771: Difference between revisions

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|tf_chipseq_enrich=GATA3#2625;2:18.1576775714707:0.00394454681927962:0.0189496101774951!NFYB#4801;2:11.1731955023576:0.0102546713505453:0.0381283641703015
|tf_chipseq_enrich=GATA3#2625;2:18.1576775714707:0.00394454681927962:0.0189496101774951!NFYB#4801;2:11.1731955023576:0.0102546713505453:0.0381283641703015
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}}
}}

Revision as of 16:20, 26 November 2012


Full id: C3771_mesothelioma_testicular_adult_neuroblastoma_testis_choriocarcinoma_teratocarcinoma



Phase1 CAGE Peaks

Hg19::chr19:22966893..22966924,-p2@ZNF99
Hg19::chr19:22966925..22966958,-p1@ZNF99
Hg19::chr19:38346040..38346055,+p@chr19:38346040..38346055
+


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
germ line cell4.02e-127
germ cell4.02e-127
Uber Anatomy
Ontology termp-valuen
adult organism1.50e-21114
neural tube2.52e-2056
neural rod2.52e-2056
future spinal cord2.52e-2056
neural keel2.52e-2056
nervous system3.77e-2089
central nervous system5.74e-1981
regional part of nervous system1.86e-1853
regional part of brain1.86e-1853
brain1.46e-1668
future brain1.46e-1668
neural plate9.86e-1582
presumptive neural plate9.86e-1582
regional part of forebrain1.47e-1441
forebrain1.47e-1441
anterior neural tube1.47e-1441
future forebrain1.47e-1441
neurectoderm1.16e-1386
brain grey matter5.60e-1334
gray matter5.60e-1334
telencephalon8.06e-1334
regional part of telencephalon2.98e-1232
cerebral hemisphere2.98e-1232
structure with developmental contribution from neural crest4.39e-11132
regional part of cerebral cortex6.46e-1122
cerebral cortex6.80e-1125
pallium6.80e-1125
ecto-epithelium7.46e-11104
testis2.00e-108
neocortex2.93e-1020
pre-chordal neural plate4.28e-1061
ectoderm-derived structure8.01e-10171
ectoderm8.01e-10171
presumptive ectoderm8.01e-10171
male reproductive organ1.69e-0911
organ system subdivision9.82e-09223
brainstem7.52e-086
posterior neural tube4.63e-0715
chordal neural plate4.63e-0715


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

(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
GATA3#2625218.15767757147070.003944546819279620.0189496101774951
NFYB#4801211.17319550235760.01025467135054530.0381283641703015



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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