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Coexpression cluster:C2511: Difference between revisions

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|tf_chipseq_enrich=IRF3#3661;2:23.4909761057448:0.00264110142537554:0.0145943910986664!NR2C2#7182;2:16.3073054526204:0.00541182534464822:0.0245560076104495!PBX3#5090;2:10.9572563433721:0.0117453018068803:0.0428425389567189!SP2#6668;2:13.0767652469223:0.00833003653661494:0.0328084129368906!SREBF1#6720;2:23.5029247202441:0.00263845490076824:0.0145843967069617
|tf_chipseq_enrich=IRF3#3661;2:23.4909761057448:0.00264110142537554:0.0145943910986664!NR2C2#7182;2:16.3073054526204:0.00541182534464822:0.0245560076104495!PBX3#5090;2:10.9572563433721:0.0117453018068803:0.0428425389567189!SP2#6668;2:13.0767652469223:0.00833003653661494:0.0328084129368906!SREBF1#6720;2:23.5029247202441:0.00263845490076824:0.0145843967069617
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}}
}}

Revision as of 15:33, 26 November 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
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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>cell_data<br>uberon_data<br><br>


Cell Type
Ontology termp-valuen
stuff accumulating cell2.20e-0787
Uber Anatomy
Ontology termp-valuen
adult organism4.63e-29114
central nervous system9.18e-2981
nervous system7.34e-2889
neural tube1.15e-2556
neural rod1.15e-2556
future spinal cord1.15e-2556
neural keel1.15e-2556
brain3.28e-2568
future brain3.28e-2568
regional part of nervous system6.84e-2453
regional part of brain6.84e-2453
neural plate1.24e-2382
presumptive neural plate1.24e-2382
neurectoderm3.35e-2186
ectoderm-derived structure1.36e-20171
ectoderm1.36e-20171
presumptive ectoderm1.36e-20171
regional part of forebrain1.99e-2041
forebrain1.99e-2041
anterior neural tube1.99e-2041
future forebrain1.99e-2041
brain grey matter7.03e-2034
gray matter7.03e-2034
telencephalon7.34e-2034
pre-chordal neural plate1.03e-1861
regional part of telencephalon1.21e-1832
cerebral hemisphere1.59e-1832
organ3.79e-18503
ecto-epithelium2.36e-17104
organ system subdivision5.13e-17223
multi-cellular organism8.98e-17656
cerebral cortex8.24e-1525
pallium8.24e-1525
embryo2.75e-14592
developing anatomical structure3.18e-14581
regional part of cerebral cortex3.63e-1322
anatomical system6.97e-13624
germ layer1.10e-12560
germ layer / neural crest1.10e-12560
embryonic tissue1.10e-12560
presumptive structure1.10e-12560
germ layer / neural crest derived structure1.10e-12560
epiblast (generic)1.10e-12560
structure with developmental contribution from neural crest1.11e-12132
anatomical group1.50e-12625
embryonic structure2.68e-12564
neocortex7.52e-1220
organ part3.23e-09218
multi-tissue structure1.93e-08342
anatomical cluster1.85e-07373


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.