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Coexpression cluster:C272: Difference between revisions

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|full_id=C272_CD19_CD4_CD8_Whole_Peripheral_lymph_tonsil
|full_id=C272_CD19_CD4_CD8_Whole_Peripheral_lymph_tonsil
|id=C272
|id=C272
|ontology_enrichment_celltype=CL:0000037!1.03e-52!172;CL:0000566!1.03e-52!172;CL:0000988!1.02e-50!182;CL:0000738!8.21e-50!140;CL:0002032!1.06e-48!165;CL:0000837!1.06e-48!165;CL:0002087!1.21e-40!119;CL:0002031!7.76e-40!124;CL:0000542!2.31e-28!53;CL:0000051!2.31e-28!53;CL:0000838!7.74e-28!52;CL:0000763!7.30e-21!112;CL:0000049!7.30e-21!112;CL:0000766!8.84e-17!76;CL:0002057!1.32e-14!42;CL:0000945!3.03e-14!24;CL:0000826!3.03e-14!24;CL:0000557!3.64e-14!71;CL:0000839!3.20e-13!70;CL:0000084!4.85e-13!25;CL:0000827!4.85e-13!25;CL:0002009!6.90e-13!65;CL:0002194!2.47e-12!63;CL:0000576!2.47e-12!63;CL:0000040!2.47e-12!63;CL:0000559!2.47e-12!63;CL:0000791!3.08e-12!18;CL:0000789!3.08e-12!18;CL:0002420!3.08e-12!18;CL:0002419!3.08e-12!18;CL:0000790!3.08e-12!18;CL:0000860!1.82e-11!45;CL:0000236!6.04e-10!14;CL:0000625!4.47e-08!11
|ontology_enrichment_disease=DOID:2531!1.51e-07!51;DOID:0060083!1.51e-07!51
|ontology_enrichment_uberon=UBERON:0002193!1.09e-21!112;UBERON:0002390!1.38e-21!102;UBERON:0003061!1.38e-21!102;UBERON:0007023!1.47e-14!115;UBERON:0002371!3.94e-12!80;UBERON:0002405!1.11e-11!115;UBERON:0001474!4.27e-11!86;UBERON:0000178!1.21e-08!15;UBERON:0000179!1.21e-08!15;UBERON:0000463!1.21e-08!15;UBERON:0004765!5.14e-07!101;UBERON:0001434!5.14e-07!101
}}
}}

Revision as of 14:27, 21 May 2012


Full id: C272_CD19_CD4_CD8_Whole_Peripheral_lymph_tonsil



Phase1 CAGE Peaks

Hg19::chr10:111836795..111836820,+p5@ADD3
Hg19::chr11:10562868..10562896,+p1@ENST00000529979
Hg19::chr11:64511738..64511759,+p@chr11:64511738..64511759
+
Hg19::chr11:64512273..64512337,-p3@RASGRP2
Hg19::chr11:94964744..94964758,+p1@ENST00000540692
Hg19::chr12:103835454..103835475,-p4@C12orf42
Hg19::chr12:103835494..103835510,-p5@C12orf42
Hg19::chr12:12867280..12867310,+p@chr12:12867280..12867310
+
Hg19::chr12:92539858..92539862,+p1@uc001tca.2
Hg19::chr12:92539926..92539990,+p1@ENST00000499685
Hg19::chr12:92540055..92540069,+p@chr12:92540055..92540069
+
Hg19::chr13:103498907..103498922,-p@chr13:103498907..103498922
-
Hg19::chr15:75081804..75081827,-p@chr15:75081804..75081827
-
Hg19::chr15:89178835..89178856,+p7@ISG20
Hg19::chr15:89178857..89178898,+p3@ISG20
Hg19::chr17:26874766..26874781,-p5@UNC119
Hg19::chr17:38020516..38020544,-p5@IKZF3
Hg19::chr17:76128488..76128519,-p4@TMC6
Hg19::chr19:16482478..16482486,-p@chr19:16482478..16482486
-
Hg19::chr19:50004358..50004377,-p2@MIR150
Hg19::chr19:7413915..7413935,+p@chr19:7413915..7413935
+
Hg19::chr1:157670686..157670730,-p2@FCRL3
Hg19::chr1:157670738..157670753,-p3@FCRL3
Hg19::chr1:207085241..207085281,-p@chr1:207085241..207085281
-
Hg19::chr1:207095279..207095310,-p1@FAIM3
Hg19::chr1:207095324..207095357,-p2@FAIM3
Hg19::chr1:207096529..207096554,-p5@FAIM3
Hg19::chr1:207096713..207096727,+p@chr1:207096713..207096727
+
Hg19::chr20:57698436..57698458,+p@chr20:57698436..57698458
+
Hg19::chr20:62266805..62266812,-p@chr20:62266805..62266812
-
Hg19::chr20:62273068..62273079,-p10@STMN3
Hg19::chr20:62273138..62273178,-p5@STMN3
Hg19::chr2:234327537..234327560,+p6@DGKD
Hg19::chr3:32433154..32433217,+p3@CMTM7
Hg19::chr3:71355163..71355209,-p5@FOXP1
Hg19::chr5:118668891..118668933,+p5@TNFAIP8
Hg19::chr6:133084580..133084605,-p2@VNN2
Hg19::chr6:24936227..24936236,-p5@FAM65B
Hg19::chr6:26285304..26285323,-p12@HIST1H4H
Hg19::chr6:31540403..31540430,-p1@LOC100287329
Hg19::chr7:139929994..139930043,+p@chr7:139929994..139930043
+
Hg19::chr7:99819057..99819097,+p@chr7:99819057..99819097
+
Hg19::chr8:134511587..134511621,-p6@ST3GAL1
Hg19::chr9:36144997..36145021,-p@chr9:36144997..36145021
-
Hg19::chrX:134429952..134429971,-p3@ZNF75D
Hg19::chrX:78200673..78200687,-p@chrX:78200673..78200687
-
Hg19::chrX:78200857..78200909,+p1@P2RY10


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>disease_data<br>


Cell Type
Ontology termp-valuen
hematopoietic stem cell1.03e-52172
angioblastic mesenchymal cell1.03e-52172
hematopoietic cell1.02e-50182
leukocyte8.21e-50140
hematopoietic oligopotent progenitor cell1.06e-48165
hematopoietic multipotent progenitor cell1.06e-48165
nongranular leukocyte1.21e-40119
hematopoietic lineage restricted progenitor cell7.76e-40124
lymphocyte2.31e-2853
common lymphoid progenitor2.31e-2853
lymphoid lineage restricted progenitor cell7.74e-2852
myeloid cell7.30e-21112
common myeloid progenitor7.30e-21112
myeloid leukocyte8.84e-1776
CD14-positive, CD16-negative classical monocyte1.32e-1442
lymphocyte of B lineage3.03e-1424
pro-B cell3.03e-1424
granulocyte monocyte progenitor cell3.64e-1471
myeloid lineage restricted progenitor cell3.20e-1370
T cell4.85e-1325
pro-T cell4.85e-1325
macrophage dendritic cell progenitor6.90e-1365
monopoietic cell2.47e-1263
monocyte2.47e-1263
monoblast2.47e-1263
promonocyte2.47e-1263
mature alpha-beta T cell3.08e-1218
alpha-beta T cell3.08e-1218
immature T cell3.08e-1218
mature T cell3.08e-1218
immature alpha-beta T cell3.08e-1218
classical monocyte1.82e-1145
B cell6.04e-1014
CD8-positive, alpha-beta T cell4.47e-0811
Uber Anatomy
Ontology termp-valuen
hemolymphoid system1.09e-21112
hematopoietic system1.38e-21102
blood island1.38e-21102
adult organism1.47e-14115
bone marrow3.94e-1280
immune system1.11e-11115
bone element4.27e-1186
blood1.21e-0815
haemolymphatic fluid1.21e-0815
organism substance1.21e-0815
skeletal element5.14e-07101
skeletal system5.14e-07101
Disease
Ontology termp-valuen
hematologic cancer1.51e-0751
immune system cancer1.51e-0751


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


No analysis results for this cluster

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


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