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Coexpression cluster:C3366: Difference between revisions

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|full_id=C3366_Mast_Neutrophils_Eosinophils_CD4_Basophils_CD19_lung
|full_id=C3366_Mast_Neutrophils_Eosinophils_CD4_Basophils_CD19_lung
|id=C3366
|id=C3366
|ontology_enrichment_celltype=CL:0000738!1.40e-32!140;CL:0000037!3.39e-30!172;CL:0000566!3.39e-30!172;CL:0002032!7.84e-28!165;CL:0000837!7.84e-28!165;CL:0000988!3.06e-26!182;CL:0002031!3.25e-26!124;CL:0002087!1.56e-23!119;CL:0000766!9.09e-18!76;CL:0000763!3.49e-16!112;CL:0000049!3.49e-16!112;CL:0000557!1.46e-14!71;CL:0000839!2.73e-14!70;CL:0002057!1.56e-13!42;CL:0000860!2.74e-12!45;CL:0002009!8.33e-12!65;CL:0000838!2.04e-11!52;CL:0002194!2.83e-11!63;CL:0000576!2.83e-11!63;CL:0000040!2.83e-11!63;CL:0000559!2.83e-11!63;CL:0000791!2.85e-11!18;CL:0000789!2.85e-11!18;CL:0002420!2.85e-11!18;CL:0002419!2.85e-11!18;CL:0000790!2.85e-11!18;CL:0000542!3.10e-11!53;CL:0000051!3.10e-11!53;CL:0000084!3.47e-08!25;CL:0000827!3.47e-08!25;CL:0000625!4.41e-08!11
|ontology_enrichment_celltype=CL:0000738!3.26e-33!136;CL:0000037!2.66e-30!168;CL:0000566!2.66e-30!168;CL:0002032!2.37e-28!161;CL:0000837!2.37e-28!161;CL:0000988!2.12e-27!177;CL:0002031!1.07e-26!120;CL:0002087!3.56e-24!115;CL:0000766!4.76e-19!72;CL:0000763!5.47e-17!108;CL:0000049!5.47e-17!108;CL:0000557!8.58e-16!67;CL:0000839!5.37e-15!66;CL:0000860!3.90e-14!42;CL:0002057!3.90e-14!42;CL:0002009!5.00e-13!61;CL:0000473!7.67e-13!48;CL:0000234!7.67e-13!48;CL:0002194!2.54e-12!59;CL:0000576!2.54e-12!59;CL:0000040!2.54e-12!59;CL:0000559!2.54e-12!59;CL:0002242!4.40e-11!55;CL:0000838!4.65e-11!52;CL:0000542!7.15e-11!53;CL:0000051!7.15e-11!53;CL:0000791!1.07e-10!18;CL:0000789!1.07e-10!18;CL:0002420!1.07e-10!18;CL:0002419!1.07e-10!18;CL:0000790!1.07e-10!18;CL:0000625!8.52e-08!11;CL:0000084!1.15e-07!25;CL:0000827!1.15e-07!25
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0007023!9.19e-30!115;UBERON:0002390!1.61e-17!102;UBERON:0003061!1.61e-17!102;UBERON:0002193!1.65e-15!112;UBERON:0001049!1.92e-11!57;UBERON:0005068!1.92e-11!57;UBERON:0006241!1.92e-11!57;UBERON:0007135!1.92e-11!57;UBERON:0002371!1.05e-10!80;UBERON:0001474!2.97e-10!86;UBERON:0003080!5.01e-10!42;UBERON:0002780!5.42e-10!41;UBERON:0001890!5.42e-10!41;UBERON:0006240!5.42e-10!41;UBERON:0001017!6.68e-09!82;UBERON:0002616!1.53e-08!59;UBERON:0005743!3.21e-08!86;UBERON:0004765!5.92e-08!101;UBERON:0001434!5.92e-08!101;UBERON:0002405!9.59e-08!115;UBERON:0000955!1.32e-07!69;UBERON:0006238!1.32e-07!69;UBERON:0002020!1.60e-07!34;UBERON:0003528!1.60e-07!34;UBERON:0001893!1.92e-07!34;UBERON:0000178!2.77e-07!15;UBERON:0000179!2.77e-07!15;UBERON:0000463!2.77e-07!15;UBERON:0002791!2.91e-07!33;UBERON:0000073!3.32e-07!94;UBERON:0001016!3.32e-07!94;UBERON:0001869!9.30e-07!32
|ontology_enrichment_uberon=UBERON:0007023!8.25e-27!114;UBERON:0002390!1.33e-18!98;UBERON:0003061!1.33e-18!98;UBERON:0002193!2.50e-16!108;UBERON:0002371!1.08e-11!76;UBERON:0002405!2.99e-11!93;UBERON:0001474!4.86e-11!82;UBERON:0001049!8.42e-11!56;UBERON:0005068!8.42e-11!56;UBERON:0006241!8.42e-11!56;UBERON:0007135!8.42e-11!56;UBERON:0000073!5.67e-10!53;UBERON:0002616!5.67e-10!53;UBERON:0002780!1.80e-09!41;UBERON:0001890!1.80e-09!41;UBERON:0003080!1.80e-09!41;UBERON:0006240!1.80e-09!41;UBERON:0004765!1.81e-09!90;UBERON:0001017!1.73e-08!81;UBERON:0001434!2.07e-08!100;UBERON:0000955!1.90e-07!68;UBERON:0006238!1.90e-07!68;UBERON:0000178!2.43e-07!15;UBERON:0000179!2.43e-07!15;UBERON:0000463!2.43e-07!15;UBERON:0001016!4.83e-07!89;UBERON:0001893!5.76e-07!34;UBERON:0003528!7.32e-07!34;UBERON:0002020!7.32e-07!34
|tf_chipseq_enrich=ELF1#1997;3:4.25809795880754:0.0129517987505461:0.0460813827658337!GABPB1#2553;3:7.06768383618217:0.00283221282541742:0.0153794766949394!MYC#4609;3:5.2222818716094:0.00702084375574015:0.0293675865510151!NFKB1#4790;3:5.48806342419384:0.00604938181565543:0.0269007658794702!PAX5#5079;3:6.66956553117783:0.00337029099967726:0.0172552488707924!PBX3#5090;2:14.6096751244961:0.00605612247321789:0.0268142858648636!SIX5#147912;2:11.391143570306:0.00987382008142903:0.037061957140755!SP1#6667;3:5.6983813781409:0.00540396270171217:0.024582275386738!YY1#7528;3:4.91117074985386:0.00844145534180826:0.0328471369017553
|tf_chipseq_enrich=ELF1#1997;3:4.25809795880754:0.0129517987505461:0.0460813827658337!GABPB1#2553;3:7.06768383618217:0.00283221282541742:0.0153794766949394!MYC#4609;3:5.2222818716094:0.00702084375574015:0.0293675865510151!NFKB1#4790;3:5.48806342419384:0.00604938181565543:0.0269007658794702!PAX5#5079;3:6.66956553117783:0.00337029099967726:0.0172552488707924!PBX3#5090;2:14.6096751244961:0.00605612247321789:0.0268142858648636!SIX5#147912;2:11.391143570306:0.00987382008142903:0.037061957140755!SP1#6667;3:5.6983813781409:0.00540396270171217:0.024582275386738!YY1#7528;3:4.91117074985386:0.00844145534180826:0.0328471369017553
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}}
}}

Revision as of 15:02, 19 October 2012


Full id: C3366_Mast_Neutrophils_Eosinophils_CD4_Basophils_CD19_lung



Phase1 CAGE Peaks

Hg19::chr13:33112956..33112967,-p3@N4BP2L2
Hg19::chr19:58144529..58144579,+p1@ZNF211
Hg19::chr2:201729393..201729428,-p2@CLK1


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><br>


Cell Type
Ontology termp-valuen
leukocyte3.26e-33136
hematopoietic stem cell2.66e-30168
angioblastic mesenchymal cell2.66e-30168
hematopoietic oligopotent progenitor cell2.37e-28161
hematopoietic multipotent progenitor cell2.37e-28161
hematopoietic cell2.12e-27177
hematopoietic lineage restricted progenitor cell1.07e-26120
nongranular leukocyte3.56e-24115
myeloid leukocyte4.76e-1972
myeloid cell5.47e-17108
common myeloid progenitor5.47e-17108
granulocyte monocyte progenitor cell8.58e-1667
myeloid lineage restricted progenitor cell5.37e-1566
classical monocyte3.90e-1442
CD14-positive, CD16-negative classical monocyte3.90e-1442
macrophage dendritic cell progenitor5.00e-1361
defensive cell7.67e-1348
phagocyte7.67e-1348
monopoietic cell2.54e-1259
monocyte2.54e-1259
monoblast2.54e-1259
promonocyte2.54e-1259
nucleate cell4.40e-1155
lymphoid lineage restricted progenitor cell4.65e-1152
lymphocyte7.15e-1153
common lymphoid progenitor7.15e-1153
mature alpha-beta T cell1.07e-1018
alpha-beta T cell1.07e-1018
immature T cell1.07e-1018
mature T cell1.07e-1018
immature alpha-beta T cell1.07e-1018
CD8-positive, alpha-beta T cell8.52e-0811
T cell1.15e-0725
pro-T cell1.15e-0725
Uber Anatomy
Ontology termp-valuen
adult organism8.25e-27114
hematopoietic system1.33e-1898
blood island1.33e-1898
hemolymphoid system2.50e-16108
bone marrow1.08e-1176
immune system2.99e-1193
bone element4.86e-1182
neural tube8.42e-1156
neural rod8.42e-1156
future spinal cord8.42e-1156
neural keel8.42e-1156
regional part of nervous system5.67e-1053
regional part of brain5.67e-1053
regional part of forebrain1.80e-0941
forebrain1.80e-0941
anterior neural tube1.80e-0941
future forebrain1.80e-0941
skeletal element1.81e-0990
central nervous system1.73e-0881
skeletal system2.07e-08100
brain1.90e-0768
future brain1.90e-0768
blood2.43e-0715
haemolymphatic fluid2.43e-0715
organism substance2.43e-0715
nervous system4.83e-0789
telencephalon5.76e-0734
brain grey matter7.32e-0734
gray matter7.32e-0734


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
ELF1#199734.258097958807540.01295179875054610.0460813827658337
GABPB1#255337.067683836182170.002832212825417420.0153794766949394
MYC#460935.22228187160940.007020843755740150.0293675865510151
NFKB1#479035.488063424193840.006049381815655430.0269007658794702
PAX5#507936.669565531177830.003370290999677260.0172552488707924
PBX3#5090214.60967512449610.006056122473217890.0268142858648636
SIX5#147912211.3911435703060.009873820081429030.037061957140755
SP1#666735.69838137814090.005403962701712170.024582275386738
YY1#752834.911170749853860.008441455341808260.0328471369017553



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.