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Coexpression cluster:C4608: Difference between revisions

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|tf_chipseq_enrich=JUND#3727;3:6.99466394187103:0.00292184504273499:0.0157588604843111!STAT3#6774;3:10.5194649971542:0.000858918453041531:0.00645263877983056!TRIM28#10155;3:18.5905250452625:0.000155596929725528:0.00197982306817792
|tf_chipseq_enrich=JUND#3727;3:6.99466394187103:0.00292184504273499:0.0157588604843111!STAT3#6774;3:10.5194649971542:0.000858918453041531:0.00645263877983056!TRIM28#10155;3:18.5905250452625:0.000155596929725528:0.00197982306817792
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}}
}}

Revision as of 16:50, 26 November 2012


Full id: C4608_myeloma_CD4_anaplastic_liposarcoma_pons_Fibroblast_adult



Phase1 CAGE Peaks

Hg19::chr6:46293524..46293563,-p10@RCAN2
Hg19::chr6:46293579..46293596,-p11@RCAN2
Hg19::chr6:46293606..46293620,-p18@RCAN2


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
neural tube8.41e-3556
neural rod8.41e-3556
future spinal cord8.41e-3556
neural keel8.41e-3556
regional part of nervous system6.20e-3353
regional part of brain6.20e-3353
neural plate3.69e-2882
presumptive neural plate3.69e-2882
brain9.86e-2868
future brain9.86e-2868
neurectoderm2.92e-2686
brain grey matter3.10e-2534
gray matter3.10e-2534
telencephalon4.58e-2534
cerebral hemisphere6.98e-2532
central nervous system1.77e-2481
regional part of forebrain3.59e-2341
forebrain3.59e-2341
anterior neural tube3.59e-2341
future forebrain3.59e-2341
regional part of cerebral cortex4.96e-2322
neocortex7.44e-2320
regional part of telencephalon2.23e-2232
nervous system6.86e-2189
ecto-epithelium7.80e-21104
pre-chordal neural plate1.43e-2061
cerebral cortex1.01e-1925
pallium1.01e-1925
adult organism8.62e-18114
structure with developmental contribution from neural crest1.65e-17132
posterior neural tube7.21e-1315
chordal neural plate7.21e-1315
gyrus9.14e-126
segmental subdivision of hindbrain3.47e-1112
hindbrain3.47e-1112
presumptive hindbrain3.47e-1112
ectoderm-derived structure2.31e-10171
ectoderm2.31e-10171
presumptive ectoderm2.31e-10171
segmental subdivision of nervous system3.62e-1013
occipital lobe8.86e-105
regional part of metencephalon1.12e-099
metencephalon1.12e-099
future metencephalon1.12e-099
organ system subdivision9.07e-09223
atypical epithelium2.62e-084
brainstem7.28e-086
neural nucleus5.79e-079
nucleus of brain5.79e-079
parietal lobe7.37e-075
frontal cortex8.59e-073
pons9.26e-073


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
JUND#372736.994663941871030.002921845042734990.0157588604843111
STAT3#6774310.51946499715420.0008589184530415310.00645263877983056
TRIM28#10155318.59052504526250.0001555969297255280.00197982306817792



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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