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Coexpression cluster:C4512: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002193!4.03e-29!112;UBERON:0002390!1.06e-27!102;UBERON:0003061!1.06e-27!102;UBERON:0002371!1.39e-18!80;UBERON:0001474!1.33e-17!86;UBERON:0002405!2.67e-16!115;UBERON:0004765!9.17e-13!101;UBERON:0001434!9.17e-13!101;UBERON:0003081!9.45e-11!216;UBERON:0000178!1.09e-07!15;UBERON:0000179!1.09e-07!15;UBERON:0000463!1.09e-07!15
|ontology_enrichment_uberon=UBERON:0002193!4.03e-29!112;UBERON:0002390!1.06e-27!102;UBERON:0003061!1.06e-27!102;UBERON:0002371!1.39e-18!80;UBERON:0001474!1.33e-17!86;UBERON:0002405!2.67e-16!115;UBERON:0004765!9.17e-13!101;UBERON:0001434!9.17e-13!101;UBERON:0003081!9.45e-11!216;UBERON:0000178!1.09e-07!15;UBERON:0000179!1.09e-07!15;UBERON:0000463!1.09e-07!15
|tf_chipseq_enrich=ATF3#467;2:14.9754496840058:0.00576829454079388:0.0259692608649871!BRCA1#672;2:13.4561537621492:0.00711980771608456:0.0296426389499763!IRF3#3661;2:31.3213014743264:0.00133951467332011:0.00887900310782429!MAFK#7975;2:18.0671554252199:0.00398367474493681:0.0191173554512914!NFYA#4800;2:12.2837204665537:0.00851601140372443:0.0324908203037033!NFYB#4801;2:11.1731955023576:0.0102546713505453:0.0381514541600028!NR3C1#2908;2:9.98201555411536:0.0127847436554717:0.046074045639538!SIX5#147912;2:11.391143570306:0.00987382008142903:0.0370886165833825
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}}
}}

Revision as of 13:08, 5 September 2012


Full id: C4512_CD4_Neutrophils_CD14_plasma_CD8_Peripheral_Eosinophils



Phase1 CAGE Peaks

Hg19::chr5:64859206..64859218,+p3@PPWD1
Hg19::chr5:64859227..64859241,+p2@PPWD1
Hg19::chrX:11778228..11778347,+p2@MSL3


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:0003755peptidyl-prolyl cis-trans isomerase activity0.0406216884493112
GO:0016859cis-trans isomerase activity0.0406216884493112
GO:0005681spliceosome0.0406216884493112
GO:0008380RNA splicing0.0406216884493112
GO:0006397mRNA processing0.0406216884493112
GO:0016853isomerase activity0.0406216884493112
GO:0016071mRNA metabolic process0.0406216884493112
GO:0006457protein folding0.0406216884493112



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
leukocyte4.24e-53140
hematopoietic stem cell1.41e-49172
angioblastic mesenchymal cell1.41e-49172
hematopoietic cell3.09e-46182
hematopoietic oligopotent progenitor cell8.55e-46165
hematopoietic multipotent progenitor cell8.55e-46165
nongranular leukocyte1.03e-44119
hematopoietic lineage restricted progenitor cell2.06e-42124
myeloid leukocyte8.53e-2676
myeloid cell5.46e-24112
common myeloid progenitor5.46e-24112
CD14-positive, CD16-negative classical monocyte1.20e-2242
granulocyte monocyte progenitor cell1.53e-2271
macrophage dendritic cell progenitor1.81e-2265
classical monocyte7.23e-2245
monopoietic cell1.17e-2163
monocyte1.17e-2163
monoblast1.17e-2163
promonocyte1.17e-2163
myeloid lineage restricted progenitor cell1.04e-2070
lymphocyte2.08e-2053
common lymphoid progenitor2.08e-2053
lymphoid lineage restricted progenitor cell5.25e-2052
mature alpha-beta T cell2.10e-1118
alpha-beta T cell2.10e-1118
immature T cell2.10e-1118
mature T cell2.10e-1118
immature alpha-beta T cell2.10e-1118
lymphocyte of B lineage4.51e-1024
pro-B cell4.51e-1024
T cell1.20e-0925
pro-T cell1.20e-0925
B cell5.86e-0814
CD8-positive, alpha-beta T cell6.01e-0811
mesenchymal cell3.17e-07358
Uber Anatomy
Ontology termp-valuen
hemolymphoid system4.03e-29112
hematopoietic system1.06e-27102
blood island1.06e-27102
bone marrow1.39e-1880
bone element1.33e-1786
immune system2.67e-16115
skeletal element9.17e-13101
skeletal system9.17e-13101
lateral plate mesoderm9.45e-11216
blood1.09e-0715
haemolymphatic fluid1.09e-0715
organism substance1.09e-0715


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#467214.97544968400580.005768294540793880.0259692608649871
BRCA1#672213.45615376214920.007119807716084560.0296426389499763
IRF3#3661231.32130147432640.001339514673320110.00887900310782429
MAFK#7975218.06715542521990.003983674744936810.0191173554512914
NFYA#4800212.28372046655370.008516011403724430.0324908203037033
NFYB#4801211.17319550235760.01025467135054530.0381514541600028
NR3C1#290829.982015554115360.01278474365547170.046074045639538
SIX5#147912211.3911435703060.009873820081429030.0370886165833825



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.