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Coexpression cluster:C4459: Difference between revisions

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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C4459_Eosinophils_Neutrophils_CD14_occipital_postcentral_parietal_medial
|full_id=C4459_Eosinophils_Neutrophils_CD14_occipital_postcentral_parietal_medial
|gostat_on_coexpression_clusters=GO:0004864!protein phosphatase inhibitor activity!0.0243568701007585!22853$GO:0019212!phosphatase inhibitor activity!0.0243568701007585!22853$GO:0016301!kinase activity!0.0243568701007585!22853;56990$GO:0046777!protein amino acid autophosphorylation!0.0243568701007585!22853$GO:0016540!protein autoprocessing!0.0243568701007585!22853$GO:0016772!transferase activity, transferring phosphorus-containing groups!0.0249784497864923!22853;56990$GO:0019888!protein phosphatase regulator activity!0.0271223419769981!22853$GO:0019208!phosphatase regulator activity!0.0271223419769981!22853$GO:0016485!protein processing!0.0290996119542236!22853$GO:0016740!transferase activity!0.0416052735611413!22853;56990
|gostat_on_coexpression_clusters=GO:0004864!protein phosphatase inhibitor activity!0.0243568701007585!22853$GO:0019212!phosphatase inhibitor activity!0.0243568701007585!22853$GO:0016301!kinase activity!0.0243568701007585!22853;56990$GO:0046777!protein amino acid autophosphorylation!0.0243568701007585!22853$GO:0016540!protein autoprocessing!0.0243568701007585!22853$GO:0016772!transferase activity, transferring phosphorus-containing groups!0.0249784497864923!22853;56990$GO:0019888!protein phosphatase regulator activity!0.0271223419769981!22853$GO:0019208!phosphatase regulator activity!0.0271223419769981!22853$GO:0016485!protein processing!0.0290996119542236!22853$GO:0016740!transferase activity!0.0416052735611413!22853;56990

Revision as of 17:32, 12 September 2012


Full id: C4459_Eosinophils_Neutrophils_CD14_occipital_postcentral_parietal_medial



Phase1 CAGE Peaks

Hg19::chr5:130599701..130599716,+p2@CDC42SE2
Hg19::chr7:97736163..97736190,+p1@LMTK2
Hg19::chr7:97736234..97736245,+p2@LMTK2


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:0004864protein phosphatase inhibitor activity0.0243568701007585
GO:0019212phosphatase inhibitor activity0.0243568701007585
GO:0016301kinase activity0.0243568701007585
GO:0046777protein amino acid autophosphorylation0.0243568701007585
GO:0016540protein autoprocessing0.0243568701007585
GO:0016772transferase activity, transferring phosphorus-containing groups0.0249784497864923
GO:0019888protein phosphatase regulator activity0.0271223419769981
GO:0019208phosphatase regulator activity0.0271223419769981
GO:0016485protein processing0.0290996119542236
GO:0016740transferase activity0.0416052735611413



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 organism3.95e-35115
neural tube9.40e-2357
neural rod9.40e-2357
future spinal cord9.40e-2357
neural keel9.40e-2357
regional part of forebrain2.02e-1941
forebrain2.02e-1941
future forebrain2.02e-1941
anterior neural tube3.41e-1942
central nervous system9.42e-1982
regional part of brain7.32e-1859
brain5.73e-1769
future brain5.73e-1769
telencephalon1.03e-1634
gray matter1.41e-1634
brain grey matter1.41e-1634
regional part of nervous system2.18e-1694
nervous system2.18e-1694
regional part of telencephalon4.32e-1633
cerebral hemisphere4.44e-1632
regional part of cerebral cortex1.28e-1422
neocortex1.81e-1320
neural plate4.49e-1386
presumptive neural plate4.49e-1386
neurectoderm4.81e-1390
cerebral cortex2.26e-1225
pallium2.26e-1225
pre-chordal neural plate2.62e-0961
hematopoietic system7.30e-07102
blood island7.30e-07102


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
ATF3#467214.97544968400580.005768294540793880.0259681414520441
BRCA1#672213.45615376214920.007119807716084560.0296414573092623
CCNT2#90536.336201576962630.003930750035764890.0190808088768417
CHD2#1106310.34402283411690.0009033701102746880.00662363598335988
CTCFL#140690213.16431623931620.007433367036996010.030692394242778
E2F1#186934.907389214879320.008460985347239390.032703806390834
E2F6#187635.017155731697390.00791769806886330.0323785766323667
EGR1#195834.988179094810140.008056488137383440.0321985138749498
ELF1#199734.258097958807540.01295179875054610.0464309514882876
ETS1#211339.728760922202340.001085840092584840.00764332772322354
HMGN3#932438.178547723350590.001827766942164210.0109030244272726
IRF1#365937.63716375356390.002244692747297240.0128583515705889
JUND#372736.994663941871030.002921845042734990.0157409767057773
NFKB1#479035.488063424193840.006049381815655430.027050496122848
NFYA#4800212.28372046655370.008516011403724430.0324896334244228
NFYB#4801211.17319550235760.01025467135054530.0381500951511986
NR3C1#290829.982015554115360.01278474365547170.0460692765632892
PAX5#507936.669565531177830.003370290999677260.0173479458706404
PBX3#5090214.60967512449610.006056122473217890.0268564126780351
POU2F2#545239.106124057742520.001324165192682130.008848015902657
SIN3A#2594235.408884726815140.006318961977991520.0277883729849449
SMC3#9126210.02995522995520.0126656379767470.0457790816630379
SP2#6668217.43568699589640.004273568481769740.0203273315419934
YY1#752834.911170749853860.008441455341808260.0330763545600327
ZEB1#6935211.25895467836260.01010222676646330.03782413641868



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.