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Coexpression cluster:C4306: Difference between revisions

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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C4306_Mast_hippocampus_amygdala_occipital_caudate_putamen_parietal
|full_id=C4306_Mast_hippocampus_amygdala_occipital_caudate_putamen_parietal
|id=C4306
|id=C4306

Revision as of 17:22, 12 September 2012


Full id: C4306_Mast_hippocampus_amygdala_occipital_caudate_putamen_parietal



Phase1 CAGE Peaks

Hg19::chr3:171178104..171178119,-p2@TNIK
Hg19::chr3:171178157..171178225,-p1@TNIK
Hg19::chr3:171178228..171178242,-p4@TNIK


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
mature alpha-beta T cell1.45e-0718
alpha-beta T cell1.45e-0718
immature T cell1.45e-0718
mature T cell1.45e-0718
immature alpha-beta T cell1.45e-0718
T cell8.25e-0725
pro-T cell8.25e-0725
Uber Anatomy
Ontology termp-valuen
adult organism1.70e-28115
neural tube2.96e-2557
neural rod2.96e-2557
future spinal cord2.96e-2557
neural keel2.96e-2557
central nervous system7.24e-2482
regional part of nervous system2.36e-2394
nervous system2.36e-2394
regional part of brain2.72e-2259
brain6.50e-2169
future brain6.50e-2169
regional part of forebrain9.64e-2141
forebrain9.64e-2141
future forebrain9.64e-2141
anterior neural tube3.95e-2042
telencephalon2.19e-1834
gray matter2.58e-1834
brain grey matter2.58e-1834
tube7.79e-18194
regional part of telencephalon7.96e-1833
cerebral hemisphere2.07e-1732
neural plate2.32e-1786
presumptive neural plate2.32e-1786
neurectoderm1.65e-1490
regional part of cerebral cortex3.40e-1422
anatomical conduit9.76e-14241
cerebral cortex3.11e-1325
pallium3.11e-1325
neocortex5.98e-1320
pre-chordal neural plate7.58e-1361
circulatory system6.48e-09113
cardiovascular system1.05e-08110
anatomical cluster1.40e-08286
epithelium2.47e-07309
anterior region of body3.04e-07129
craniocervical region3.04e-07129
cell layer4.70e-07312
basal ganglion9.28e-079
nuclear complex of neuraxis9.28e-079
aggregate regional part of brain9.28e-079
collection of basal ganglia9.28e-079
cerebral subcortex9.28e-079


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
CCNT2#90536.336201576962630.003930750035764890.0190630881349083
CHD2#1106310.34402283411690.0009033701102746880.00661991797270405
CTCF#1066435.360256373075030.0064925092527670.0280461254022308
E2F4#1874312.66806031528440.0004917987006298980.00438101027764295
E2F6#187635.017155731697390.00791769806886330.0323431168543049
EGR1#195834.988179094810140.008056488137383440.0321665098470903
ELF1#199734.258097958807540.01295179875054610.046384778468839
IRF1#365937.63716375356390.002244692747297240.0128470772596984
MAX#414936.452555509007120.003721913834265510.0187079102385627
MXI1#460139.96157162875930.001011470541259020.00721810535418866
MYC#460935.22228187160940.007020843755740150.0295391331025962
NFKB1#479035.488063424193840.006049381815655430.0270308213513557
PAX5#507936.669565531177830.003370290999677260.0173402542842157
PBX3#5090321.91451268674419.49854535978121e-050.00137094883752099
POU2F2#545239.106124057742520.001324165192682130.00884122801166916
SP1#666735.69838137814090.005403962701712170.0247298422839417
YY1#752834.911170749853860.008441455341808260.0330453598127034
ZBTB7A#5134137.35190930787590.002516255860282270.0140614931666766
ZEB1#6935316.88843201754390.0002075486917327580.00243306519428415
ZNF263#1012738.221841637010680.001799043925565870.0109716991849445



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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