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Coexpression cluster:C2511: Difference between revisions

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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C2511_optic_substantia_corpus_hippocampus_globus_thalamus_spinal
|full_id=C2511_optic_substantia_corpus_hippocampus_globus_thalamus_spinal
|id=C2511
|id=C2511

Revision as of 15:15, 12 September 2012


Full id: C2511_optic_substantia_corpus_hippocampus_globus_thalamus_spinal



Phase1 CAGE Peaks

Hg19::chr1:109855123..109855141,-p3@SORT1
Hg19::chr1:109856077..109856090,-p@chr1:109856077..109856090
-
Hg19::chr1:109940510..109940549,-p1@SORT1
Hg19::chr1:109940550..109940565,-p2@SORT1


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
regional part of nervous system3.22e-3094
nervous system3.22e-3094
adult organism3.32e-30115
central nervous system1.82e-2982
neural tube3.30e-2657
neural rod3.30e-2657
future spinal cord3.30e-2657
neural keel3.30e-2657
brain6.92e-2669
future brain6.92e-2669
regional part of brain3.59e-2559
neural plate4.00e-2486
presumptive neural plate4.00e-2486
ectoderm-derived structure9.38e-23169
neurectoderm1.37e-2190
ectoderm3.78e-21173
presumptive ectoderm3.78e-21173
anterior neural tube9.88e-2142
regional part of forebrain2.05e-2041
forebrain2.05e-2041
future forebrain2.05e-2041
telencephalon8.94e-2034
gray matter9.22e-2034
brain grey matter9.22e-2034
organ1.15e-19511
regional part of telencephalon3.51e-1933
head8.20e-19123
cerebral hemisphere2.02e-1832
pre-chordal neural plate2.06e-1861
multi-cellular organism3.79e-17659
anterior region of body4.26e-17129
craniocervical region4.26e-17129
embryo3.30e-15612
cerebral cortex1.22e-1425
pallium1.22e-1425
embryonic structure2.83e-14605
developing anatomical structure2.83e-14605
germ layer4.31e-14604
embryonic tissue4.31e-14604
presumptive structure4.31e-14604
epiblast (generic)4.31e-14604
anatomical system3.23e-13625
regional part of cerebral cortex4.93e-1322
anatomical group7.05e-13626
neocortex9.90e-1220
organ part6.41e-10219
organism subdivision3.42e-08365


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
IRF3#3661223.49097610574480.002641101425375540.0145943910986664
NR2C2#7182216.30730545262040.005411825344648220.0245560076104495
PBX3#5090210.95725634337210.01174530180688030.0428425389567189
SP2#6668213.07676524692230.008330036536614940.0328084129368906
SREBF1#6720223.50292472024410.002638454900768240.0145843967069617



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.