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Coexpression cluster:C1214: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002390!2.03e-29!102;UBERON:0003061!2.03e-29!102;UBERON:0002193!4.80e-25!112;UBERON:0002371!3.44e-22!80;UBERON:0001474!1.09e-19!86;UBERON:0002405!4.89e-17!115;UBERON:0002384!7.04e-15!375;UBERON:0004765!9.28e-14!101;UBERON:0001434!9.28e-14!101;UBERON:0003081!5.02e-08!216;UBERON:0000178!7.63e-08!15;UBERON:0000179!7.63e-08!15;UBERON:0000463!7.63e-08!15
|ontology_enrichment_uberon=UBERON:0002390!2.03e-29!102;UBERON:0003061!2.03e-29!102;UBERON:0002193!4.80e-25!112;UBERON:0002371!3.44e-22!80;UBERON:0001474!1.09e-19!86;UBERON:0002405!4.89e-17!115;UBERON:0002384!7.04e-15!375;UBERON:0004765!9.28e-14!101;UBERON:0001434!9.28e-14!101;UBERON:0003081!5.02e-08!216;UBERON:0000178!7.63e-08!15;UBERON:0000179!7.63e-08!15;UBERON:0000463!7.63e-08!15
|tf_chipseq_enrich=BCL11A#53335;3:12.1583379015459:0.00137698016345987:0.00897077108674352!BCL3#602;3:14.8059012016021:0.000777274573558596:0.00609076974699026!CCNT2#905;5:4.52585826925902:0.0015515733062647:0.00985613798023105!EP300#2033;4:3.87082384355611:0.0114256758668448:0.0418608770735073!FOS#2353;4:5.14168874793966:0.00404209586567825:0.019348815203757!FOSL2#2355;3:7.25580025909787:0.00602077509384975:0.0269861263476492!HMGN3#9324;4:4.67345584191462:0.00575188109993887:0.0259098861417518!JUN#3725;4:7.15018810990648:0.00117132817770777:0.00795864573232855!JUNB#3726;3:13.1188425684948:0.0011047899931696:0.00767838970497372!MEF2C#4208;2:11.8032441407497:0.0113453818123496:0.0416002644068385!NFKB1#4790;5:3.9200453029956:0.00303658142448461:0.0161196262779174!PAX5#5079;5:4.76397537941274:0.00121882104700747:0.00820077640306745!POU2F2#5452;4:5.20349946156716:0.00386671431017981:0.0190659447543019!SP1#6667;5:4.07027241295778:0.00254920612899158:0.0141112280121774!SPI1#6688;4:4.68818486201299:0.00568568052914417:0.0256670321496991!SRF#6722;3:5.91307639807192:0.0106686813016745:0.0393942301819257!TCF12#6938;5:7.59604635870459:0.000131112637393808:0.00172459354367404!TCF7L2#6934;4:6.15438660750705:0.00206467614813804:0.01197227873163!ZEB1#6935;3:7.23789943609022:0.0060628079203571:0.02683364819232
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}}
}}

Revision as of 12:49, 5 September 2012


Full id: C1214_Eosinophils_Natural_CD14_Basophils_Neutrophils_Mast_CD34



Phase1 CAGE Peaks

Hg19::chr15:94850232..94850237,+p@chr15:94850232..94850237
+
Hg19::chr19:13957417..13957455,-p@chr19:13957417..13957455
-
Hg19::chr19:13973090..13973103,-p@chr19:13973090..13973103
-
Hg19::chr19:39894772..39894785,+p@chr19:39894772..39894785
+
Hg19::chr20:35233898..35233903,-p@chr20:35233898..35233903
-
Hg19::chr2:137000368..137000372,-p@chr2:137000368..137000372
-
Hg19::chr2:28582698..28582710,+p@chr2:28582698..28582710
+


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
leukocyte1.00e-50140
hematopoietic stem cell1.60e-50172
angioblastic mesenchymal cell1.60e-50172
hematopoietic cell3.01e-49182
hematopoietic oligopotent progenitor cell3.36e-46165
hematopoietic multipotent progenitor cell3.36e-46165
nongranular leukocyte4.42e-39119
hematopoietic lineage restricted progenitor cell2.19e-38124
myeloid cell1.06e-27112
common myeloid progenitor1.06e-27112
myeloid leukocyte2.52e-2776
CD14-positive, CD16-negative classical monocyte4.11e-2742
classical monocyte5.98e-2645
granulocyte monocyte progenitor cell2.40e-2271
macrophage dendritic cell progenitor3.42e-2165
myeloid lineage restricted progenitor cell1.72e-2070
monopoietic cell3.68e-2063
monocyte3.68e-2063
monoblast3.68e-2063
promonocyte3.68e-2063
mesenchymal cell1.15e-17358
connective tissue cell1.19e-16365
lymphocyte1.82e-1653
common lymphoid progenitor1.82e-1653
lymphoid lineage restricted progenitor cell4.09e-1652
motile cell4.23e-16390
multi fate stem cell1.12e-10430
stem cell2.16e-10444
somatic stem cell7.25e-10436
native cell6.18e-09722
T cell2.00e-0825
pro-T cell2.00e-0825
mature alpha-beta T cell7.38e-0818
alpha-beta T cell7.38e-0818
immature T cell7.38e-0818
mature T cell7.38e-0818
immature alpha-beta T cell7.38e-0818
lymphocyte of B lineage3.49e-0724
pro-B cell3.49e-0724
granulocyte6.58e-078
intermediate monocyte7.03e-079
CD14-positive, CD16-positive monocyte7.03e-079
Uber Anatomy
Ontology termp-valuen
hematopoietic system2.03e-29102
blood island2.03e-29102
hemolymphoid system4.80e-25112
bone marrow3.44e-2280
bone element1.09e-1986
immune system4.89e-17115
connective tissue7.04e-15375
skeletal element9.28e-14101
skeletal system9.28e-14101
lateral plate mesoderm5.02e-08216
blood7.63e-0815
haemolymphatic fluid7.63e-0815
organism substance7.63e-0815


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
BCL11A#53335312.15833790154590.001376980163459870.00897077108674352
BCL3#602314.80590120160210.0007772745735585960.00609076974699026
CCNT2#90554.525858269259020.00155157330626470.00985613798023105
EP300#203343.870823843556110.01142567586684480.0418608770735073
FOS#235345.141688747939660.004042095865678250.019348815203757
FOSL2#235537.255800259097870.006020775093849750.0269861263476492
HMGN3#932444.673455841914620.005751881099938870.0259098861417518
JUN#372547.150188109906480.001171328177707770.00795864573232855
JUNB#3726313.11884256849480.00110478999316960.00767838970497372
MEF2C#4208211.80324414074970.01134538181234960.0416002644068385
NFKB1#479053.92004530299560.003036581424484610.0161196262779174
PAX5#507954.763975379412740.001218821047007470.00820077640306745
POU2F2#545245.203499461567160.003866714310179810.0190659447543019
SP1#666754.070272412957780.002549206128991580.0141112280121774
SPI1#668844.688184862012990.005685680529144170.0256670321496991
SRF#672235.913076398071920.01066868130167450.0393942301819257
TCF12#693857.596046358704590.0001311126373938080.00172459354367404
TCF7L2#693446.154386607507050.002064676148138040.01197227873163
ZEB1#693537.237899436090220.00606280792035710.02683364819232



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.