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Coexpression cluster:C4448: Difference between revisions

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|tf_chipseq_enrich=E2F1#1869;3:4.90738921487932:0.00846098534723939:0.0327001757273558!ELF1#1997;3:4.25809795880754:0.0129517987505461:0.0464277641911201!GABPB1#2553;3:7.06768383618217:0.00283221282541742:0.0154630913938925!IRF1#3659;3:7.6371637535639:0.00224469274729724:0.0128576463464584!RFX5#5993;3:12.0479108271951:0.000571724605031258:0.00486003141989741!SIN3A#25942;3:5.40888472681514:0.00631896197799152:0.0277872029481876!SP1#6667;3:5.6983813781409:0.00540396270171217:0.0247558759805297!TRIM28#10155;2:12.3936833635083:0.00836834412943847:0.0329381733826194!YY1#7528;3:4.91117074985386:0.00844145534180826:0.0330726321207605
|tf_chipseq_enrich=E2F1#1869;3:4.90738921487932:0.00846098534723939:0.0327001757273558!ELF1#1997;3:4.25809795880754:0.0129517987505461:0.0464277641911201!GABPB1#2553;3:7.06768383618217:0.00283221282541742:0.0154630913938925!IRF1#3659;3:7.6371637535639:0.00224469274729724:0.0128576463464584!RFX5#5993;3:12.0479108271951:0.000571724605031258:0.00486003141989741!SIN3A#25942;3:5.40888472681514:0.00631896197799152:0.0277872029481876!SP1#6667;3:5.6983813781409:0.00540396270171217:0.0247558759805297!TRIM28#10155;2:12.3936833635083:0.00836834412943847:0.0329381733826194!YY1#7528;3:4.91117074985386:0.00844145534180826:0.0330726321207605
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}}
}}

Revision as of 16:44, 26 November 2012


Full id: C4448_Neutrophils_pons_brain_frontal_Eosinophils_Mast_spinal



Phase1 CAGE Peaks

Hg19::chr5:108745603..108745631,-p1@PJA2
Hg19::chr6:122792919..122792970,-p1@SERINC1
Hg19::chr6:122792978..122792992,-p2@SERINC1


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


GO IDGO nameFDR corrected p-value
GO:0032329serine transport0.00238428140252734
GO:0015825L-serine transport0.00238428140252734
GO:0022889serine transmembrane transporter activity0.00238428140252734
GO:0015194L-serine transmembrane transporter activity0.00238428140252734
GO:0005789endoplasmic reticulum membrane0.0025456993930067
GO:0042175nuclear envelope-endoplasmic reticulum network0.0025456993930067
GO:0044432endoplasmic reticulum part0.00270600274992411
GO:0006658phosphatidylserine metabolic process0.00476814168412872
GO:0015807L-amino acid transport0.00529777923387416
GO:0005783endoplasmic reticulum0.00575482801364196
GO:0015804neutral amino acid transport0.00617501311531734
GO:0012505endomembrane system0.00617501311531734
GO:0015175neutral amino acid transmembrane transporter activity0.00623443615742896
GO:0015179L-amino acid transmembrane transporter activity0.0106759301763204
GO:0031090organelle membrane0.0106759301763204
GO:0015171amino acid transmembrane transporter activity0.0185258503936613
GO:0006665sphingolipid metabolic process0.0185258503936613
GO:0006865amino acid transport0.0185258503936613
GO:0015837amine transport0.0200384602203091
GO:0046943carboxylic acid transmembrane transporter activity0.0200384602203091
GO:0046942carboxylic acid transport0.0200384602203091
GO:0015849organic acid transport0.0200384602203091
GO:0005342organic acid transmembrane transporter activity0.0200384602203091
GO:0006650glycerophospholipid metabolic process0.0200384602203091
GO:0051347positive regulation of transferase activity0.027268406000498
GO:0045211postsynaptic membrane0.027268406000498
GO:0044456synapse part0.0283682184882672
GO:0005886plasma membrane0.0352423033661863
GO:0006644phospholipid metabolic process0.0352423033661863
GO:0051338regulation of transferase activity0.0368541894013872
GO:0044446intracellular organelle part0.0368541894013872
GO:0044422organelle part0.0368541894013872
GO:0043085positive regulation of catalytic activity0.0368541894013872
GO:0006643membrane lipid metabolic process0.0379968989070936
GO:0044444cytoplasmic part0.0422762736071943
GO:0000139Golgi membrane0.0480896116943764



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
adult organism1.43e-34114
neural tube6.52e-2356
neural rod6.52e-2356
future spinal cord6.52e-2356
neural keel6.52e-2356
regional part of nervous system8.70e-2253
regional part of brain8.70e-2253
central nervous system1.03e-2081
regional part of forebrain1.30e-2041
forebrain1.30e-2041
anterior neural tube1.30e-2041
future forebrain1.30e-2041
brain1.19e-1968
future brain1.19e-1968
nervous system1.29e-1889
telencephalon6.54e-1734
brain grey matter8.61e-1734
gray matter8.61e-1734
cerebral hemisphere9.10e-1632
regional part of telencephalon1.11e-1532
neural plate5.78e-1482
presumptive neural plate5.78e-1482
regional part of cerebral cortex1.67e-1322
neurectoderm5.74e-1386
neocortex2.25e-1220
cerebral cortex7.40e-1225
pallium7.40e-1225
pre-chordal neural plate3.16e-1161
structure with developmental contribution from neural crest1.15e-10132
ectoderm-derived structure1.98e-09171
ectoderm1.98e-09171
presumptive ectoderm1.98e-09171
ecto-epithelium2.00e-09104
organ5.80e-08503


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
E2F1#186934.907389214879320.008460985347239390.0327001757273558
ELF1#199734.258097958807540.01295179875054610.0464277641911201
GABPB1#255337.067683836182170.002832212825417420.0154630913938925
IRF1#365937.63716375356390.002244692747297240.0128576463464584
RFX5#5993312.04791082719510.0005717246050312580.00486003141989741
SIN3A#2594235.408884726815140.006318961977991520.0277872029481876
SP1#666735.69838137814090.005403962701712170.0247558759805297
TRIM28#10155212.39368336350830.008368344129438470.0329381733826194
YY1#752834.911170749853860.008441455341808260.0330726321207605



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.