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Coexpression cluster:C3554: Difference between revisions

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|ontology_enrichment_disease=DOID:2531!4.96e-31!51;DOID:0060083!4.96e-31!51;DOID:1240!4.96e-30!39;DOID:8692!4.91e-25!31
|ontology_enrichment_disease=DOID:2531!4.96e-31!51;DOID:0060083!4.96e-31!51;DOID:1240!4.96e-30!39;DOID:8692!4.91e-25!31
|ontology_enrichment_uberon=UBERON:0002390!1.04e-31!102;UBERON:0003061!1.04e-31!102;UBERON:0002193!2.60e-28!112;UBERON:0002371!3.36e-19!80;UBERON:0001474!1.86e-16!86;UBERON:0002405!1.43e-15!115;UBERON:0002384!8.93e-12!375;UBERON:0004765!9.64e-12!101;UBERON:0001434!9.64e-12!101;UBERON:0000178!3.99e-10!15;UBERON:0000179!3.99e-10!15;UBERON:0000463!3.99e-10!15;UBERON:0007023!3.45e-09!115
|ontology_enrichment_uberon=UBERON:0002390!1.04e-31!102;UBERON:0003061!1.04e-31!102;UBERON:0002193!2.60e-28!112;UBERON:0002371!3.36e-19!80;UBERON:0001474!1.86e-16!86;UBERON:0002405!1.43e-15!115;UBERON:0002384!8.93e-12!375;UBERON:0004765!9.64e-12!101;UBERON:0001434!9.64e-12!101;UBERON:0000178!3.99e-10!15;UBERON:0000179!3.99e-10!15;UBERON:0000463!3.99e-10!15;UBERON:0007023!3.45e-09!115
|tf_chipseq_enrich=BCL11A#53335;3:28.3694551036071:4.37778126761649e-05:0.000777437676940313!EBF1#1879;3:8.906466846569:0.0014152328356098:0.00914128901714715!EGR1#1958;3:4.98817909481014:0.00805648813738344:0.0320025697771257!ELF1#1997;3:4.25809795880754:0.0129517987505461:0.0461363931139631!NFKB1#4790;3:5.48806342419384:0.00604938181565543:0.0269259882136566!PAX5#5079;3:6.66956553117783:0.00337029099967726:0.017268793686665!SP1#6667;3:5.6983813781409:0.00540396270171217:0.0246090721463381!SPI1#6688;3:8.20432350852273:0.00181059318941052:0.0108983080000487!YY1#7528;3:4.91117074985386:0.00844145534180826:0.0328753087386029!ZBTB7A#51341;3:7.3519093078759:0.00251625586028227:0.0139933570709276
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}}
}}

Revision as of 12:52, 5 September 2012


Full id: C3554_acute_myelodysplastic_Natural_chronic_Basophils_CD8_CD133



Phase1 CAGE Peaks

Hg19::chr16:29674246..29674275,+p3@SPN
Hg19::chr16:29674277..29674306,+p2@SPN
Hg19::chr16:29674323..29674335,+p8@SPN


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 cell1.33e-80172
angioblastic mesenchymal cell1.33e-80172
hematopoietic cell4.34e-75182
hematopoietic oligopotent progenitor cell3.12e-74165
hematopoietic multipotent progenitor cell3.12e-74165
leukocyte8.66e-54140
myeloid cell2.50e-47112
common myeloid progenitor2.50e-47112
hematopoietic lineage restricted progenitor cell2.40e-45124
nongranular leukocyte1.52e-42119
myeloid leukocyte5.22e-2376
lymphocyte1.92e-2253
common lymphoid progenitor1.92e-2253
granulocyte monocyte progenitor cell4.52e-2271
lymphoid lineage restricted progenitor cell5.75e-2252
myeloid lineage restricted progenitor cell4.87e-2170
T cell3.76e-1925
pro-T cell3.76e-1925
macrophage dendritic cell progenitor1.26e-1865
monopoietic cell2.39e-1763
monocyte2.39e-1763
monoblast2.39e-1763
promonocyte2.39e-1763
CD14-positive, CD16-negative classical monocyte9.03e-1742
mature alpha-beta T cell5.54e-1518
alpha-beta T cell5.54e-1518
immature T cell5.54e-1518
mature T cell5.54e-1518
immature alpha-beta T cell5.54e-1518
classical monocyte9.11e-1545
mesenchymal cell1.43e-13358
connective tissue cell1.70e-12365
CD8-positive, alpha-beta T cell8.93e-1111
motile cell3.57e-09390
Uber Anatomy
Ontology termp-valuen
hematopoietic system1.04e-31102
blood island1.04e-31102
hemolymphoid system2.60e-28112
bone marrow3.36e-1980
bone element1.86e-1686
immune system1.43e-15115
connective tissue8.93e-12375
skeletal element9.64e-12101
skeletal system9.64e-12101
blood3.99e-1015
haemolymphatic fluid3.99e-1015
organism substance3.99e-1015
adult organism3.45e-09115
Disease
Ontology termp-valuen
hematologic cancer4.96e-3151
immune system cancer4.96e-3151
leukemia4.96e-3039
myeloid leukemia4.91e-2531


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#53335328.36945510360714.37778126761649e-050.000777437676940313
EBF1#187938.9064668465690.00141523283560980.00914128901714715
EGR1#195834.988179094810140.008056488137383440.0320025697771257
ELF1#199734.258097958807540.01295179875054610.0461363931139631
NFKB1#479035.488063424193840.006049381815655430.0269259882136566
PAX5#507936.669565531177830.003370290999677260.017268793686665
SP1#666735.69838137814090.005403962701712170.0246090721463381
SPI1#668838.204323508522730.001810593189410520.0108983080000487
YY1#752834.911170749853860.008441455341808260.0328753087386029
ZBTB7A#5134137.35190930787590.002516255860282270.0139933570709276



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.

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=Coexpression_cluster:C3554&oldid=2131671"