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Coexpression cluster:C4591: Difference between revisions

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|tf_chipseq_enrich=IRF4#3662;2:14.6096751244961:0.00605612247321789:0.0268575530777241!NFKB1#4790;3:5.48806342419384:0.00604938181565543:0.0270713594757579!NFYA#4800;2:12.2837204665537:0.00851601140372443:0.0324967560010806!NFYB#4801;2:11.1731955023576:0.0102546713505453:0.0381596102465473!RFX5#5993;3:12.0479108271951:0.000571724605031258:0.00486517933878103
|tf_chipseq_enrich=IRF4#3662;2:14.6096751244961:0.00605612247321789:0.0268575530777241!NFKB1#4790;3:5.48806342419384:0.00604938181565543:0.0270713594757579!NFYA#4800;2:12.2837204665537:0.00851601140372443:0.0324967560010806!NFYB#4801;2:11.1731955023576:0.0102546713505453:0.0381596102465473!RFX5#5993;3:12.0479108271951:0.000571724605031258:0.00486517933878103
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}}
}}

Revision as of 16:50, 26 November 2012


Full id: C4591_Neutrophils_Basophils_Eosinophils_migratory_CD14_CD4_CD8



Phase1 CAGE Peaks

Hg19::chr6:31239114..31239134,-p6@HLA-C
Hg19::chr6:31239852..31239876,-p1@HLA-C
Hg19::chr6:31324943..31324963,-p1@HLA-B


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


p.valueFDRnGenesnPathwayName
5.08218999092061e-050.002680855220210622204Endocytosis (KEGG):04144
2.96743344876993e-050.001707623066428512156Phagosome (KEGG):04145
2.25318768070372e-050.001447397695246722136Cell adhesion molecules (CAMs) (KEGG):04514
7.37072179210596e-060.000583208361800384278Antigen processing and presentation (KEGG):04612
2.28656823893637e-050.001447397695246722137Natural killer cell mediated cytotoxicity (KEGG):04650
2.42990828311186e-060.00044465996176429245Type I diabetes mellitus (KEGG):04940
3.51232197286169e-060.00044465996176429254Autoimmune thyroid disease (KEGG):05320
1.81874953311705e-060.00044465996176429239Allograft rejection (KEGG):05330
2.21637088853536e-060.00044465996176429243Graft-versus-host disease (KEGG):05332
6.2735813854888e-060.00056731100243063272Viral myocarditis (KEGG):05416
4.94817686742777e-060.00052203265951363264Proteasome Degradation (Wikipathways):WP183
0.0003198274735665560.01557313775135612511Signaling in Immune system (Reactome):REACT_6900
3.12942733431072e-060.00044465996176429251{HLA-A,53} (Static Module):NA



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:0032393MHC class I receptor activity0.0216649005062993
GO:0002474antigen processing and presentation of peptide antigen via MHC class I0.0236959849287649
GO:0048002antigen processing and presentation of peptide antigen0.0236959849287649
GO:0042612MHC class I protein complex0.039098375132462
GO:0042611MHC protein complex0.0468277797401782
GO:0019882antigen processing and presentation0.0468277797401782



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
leukocyte2.17e-31136
myeloid leukocyte7.60e-2772
nongranular leukocyte2.04e-26115
defensive cell2.88e-2548
phagocyte2.88e-2548
hematopoietic lineage restricted progenitor cell1.21e-24120
macrophage dendritic cell progenitor6.84e-2461
classical monocyte1.10e-2342
CD14-positive, CD16-negative classical monocyte1.10e-2342
monopoietic cell2.86e-2359
monocyte2.86e-2359
monoblast2.86e-2359
promonocyte2.86e-2359
granulocyte monocyte progenitor cell5.72e-2367
myeloid lineage restricted progenitor cell7.68e-2166
hematopoietic stem cell1.33e-18168
angioblastic mesenchymal cell1.33e-18168
hematopoietic oligopotent progenitor cell2.46e-18161
hematopoietic multipotent progenitor cell2.46e-18161
hematopoietic cell6.46e-18177
myeloid cell1.67e-13108
common myeloid progenitor1.67e-13108
stuff accumulating cell8.99e-1187
mesenchymal cell3.43e-08354
multi fate stem cell3.26e-07427
connective tissue cell3.26e-07361
Uber Anatomy
Ontology termp-valuen
hemolymphoid system1.33e-26108
hematopoietic system2.62e-2598
blood island2.62e-2598
immune system4.98e-2293
bone marrow5.87e-1976
bone element9.88e-1882
lateral plate mesoderm1.71e-15203
skeletal element1.74e-1390
skeletal system4.21e-11100
mesoderm7.16e-09315
mesoderm-derived structure7.16e-09315
presumptive mesoderm7.16e-09315
musculoskeletal system5.03e-07167
connective tissue6.73e-07371


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
IRF4#3662214.60967512449610.006056122473217890.0268575530777241
NFKB1#479035.488063424193840.006049381815655430.0270713594757579
NFYA#4800212.28372046655370.008516011403724430.0324967560010806
NFYB#4801211.17319550235760.01025467135054530.0381596102465473
RFX5#5993312.04791082719510.0005717246050312580.00486517933878103



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.