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Coexpression cluster:C2814: Difference between revisions

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|tf_chipseq_enrich=GATA2#2624;4:12.744931733554:3.78864877853583e-05:0.000724030539398909
|tf_chipseq_enrich=GATA2#2624;4:12.744931733554:3.78864877853583e-05:0.000724030539398909
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}}
}}

Revision as of 15:44, 26 November 2012


Full id: C2814_Smooth_mesenchymal_alveolar_Preadipocyte_pancreas_leiomyoma_Mast



Phase1 CAGE Peaks

Hg19::chr5:150157847..150157859,+p6@C5orf62
Hg19::chr5:150157860..150157883,+p4@C5orf62
Hg19::chr5:150157886..150157917,+p3@C5orf62
Hg19::chr5:150157924..150157963,+p2@C5orf62


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>

Uber Anatomy
Ontology termp-valuen
artery3.23e-1542
arterial blood vessel3.23e-1542
arterial system3.23e-1542
tube2.53e-14192
muscle tissue8.39e-1464
musculature8.39e-1464
musculature of body8.39e-1464
skeletal muscle tissue1.16e-1362
striated muscle tissue1.16e-1362
myotome1.16e-1362
somite5.01e-1271
presomitic mesoderm5.01e-1271
presumptive segmental plate5.01e-1271
dermomyotome5.01e-1271
trunk paraxial mesoderm5.01e-1271
systemic artery5.77e-1233
systemic arterial system5.77e-1233
paraxial mesoderm1.07e-1172
presumptive paraxial mesoderm1.07e-1172
epithelial vesicle1.61e-1178
dense mesenchyme tissue2.22e-1173
epithelium3.93e-11306
cell layer9.17e-11309
anatomical conduit4.74e-10240
epithelial tube open at both ends4.85e-1059
blood vessel4.85e-1059
blood vasculature4.85e-1059
vascular cord4.85e-1059
splanchnic layer of lateral plate mesoderm7.42e-1083
multilaminar epithelium2.36e-0983
epithelial tube3.60e-09117
adult organism3.00e-08114
neural tube7.72e-0856
neural rod7.72e-0856
future spinal cord7.72e-0856
neural keel7.72e-0856
circulatory system7.84e-08112
multi-tissue structure9.92e-08342
vasculature1.21e-0778
vascular system1.21e-0778
trunk mesenchyme1.29e-07122
brain grey matter1.58e-0734
gray matter1.58e-0734
vessel1.58e-0768
structure with developmental contribution from neural crest1.77e-07132
telencephalon2.37e-0734
thoracic segment blood vessel2.48e-075
subclavian artery2.48e-075
primary circulatory organ2.56e-0727
regional part of nervous system2.88e-0753
regional part of brain2.88e-0753
neural plate3.10e-0782
presumptive neural plate3.10e-0782
neural nucleus6.89e-079
nucleus of brain6.89e-079
cardiovascular system8.27e-07109


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
GATA2#2624412.7449317335543.78864877853583e-050.000724030539398909



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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