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Coexpression cluster:C3231: Difference between revisions

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|tf_chipseq_enrich=BCL11A#53335;3:28.3694551036071:4.37778126761649e-05:0.000776777264370707!BCL3#602;3:34.5471028037383:2.42397750207122e-05:0.000526534497376906!CHD2#1106;3:10.3440228341169:0.000903370110274688:0.0065875625573927!CTCF#10664;3:5.36025637307503:0.006492509252767:0.0278537287976394!EBF1#1879;3:8.906466846569:0.0014152328356098:0.00912774051245923!EGR1#1958;3:4.98817909481014:0.00805648813738344:0.0319321276880527!ELF1#1997;3:4.25809795880754:0.0129517987505461:0.0460390357614881!GATA1#2623;3:13.5603081438004:0.000400961596378263:0.00387024289871991!IRF4#3662;3:21.9145126867441:9.49854535978121e-05:0.00136210157741342!MAX#4149;3:6.45255550900712:0.00372191383426551:0.018591589771229!MYC#4609;3:5.2222818716094:0.00702084375574015:0.0293405586413407!NFKB1#4790;3:5.48806342419384:0.00604938181565543:0.0268755907540088!PAX5#5079;3:6.66956553117783:0.00337029099967726:0.0172434145747952!POU2F2#5452;3:9.10612405774252:0.00132416519268213:0.00879959840662566!SP1#6667;3:5.6983813781409:0.00540396270171217:0.0245619488469021!SPI1#6688;3:8.20432350852273:0.00181059318941052:0.0108845071149971!SRF#6722;3:13.7971782621678:0.000380661502580019:0.00374067620135064!TCF12#6938;3:10.6344649021864:0.000831352399020207:0.00627987944461676!USF1#7391;3:6.36149927720796:0.0038840405729056:0.0189651369112015!USF2#7392;3:12.9921973850696:0.000455897939342781:0.0042061417744718!YY1#7528;3:4.91117074985386:0.00844145534180826:0.0328177916335286!ZEB1#6935;3:16.8884320175439:0.000207548691732758:0.00242164873375908
|tf_chipseq_enrich=BCL11A#53335;3:28.3694551036071:4.37778126761649e-05:0.000776777264370707!BCL3#602;3:34.5471028037383:2.42397750207122e-05:0.000526534497376906!CHD2#1106;3:10.3440228341169:0.000903370110274688:0.0065875625573927!CTCF#10664;3:5.36025637307503:0.006492509252767:0.0278537287976394!EBF1#1879;3:8.906466846569:0.0014152328356098:0.00912774051245923!EGR1#1958;3:4.98817909481014:0.00805648813738344:0.0319321276880527!ELF1#1997;3:4.25809795880754:0.0129517987505461:0.0460390357614881!GATA1#2623;3:13.5603081438004:0.000400961596378263:0.00387024289871991!IRF4#3662;3:21.9145126867441:9.49854535978121e-05:0.00136210157741342!MAX#4149;3:6.45255550900712:0.00372191383426551:0.018591589771229!MYC#4609;3:5.2222818716094:0.00702084375574015:0.0293405586413407!NFKB1#4790;3:5.48806342419384:0.00604938181565543:0.0268755907540088!PAX5#5079;3:6.66956553117783:0.00337029099967726:0.0172434145747952!POU2F2#5452;3:9.10612405774252:0.00132416519268213:0.00879959840662566!SP1#6667;3:5.6983813781409:0.00540396270171217:0.0245619488469021!SPI1#6688;3:8.20432350852273:0.00181059318941052:0.0108845071149971!SRF#6722;3:13.7971782621678:0.000380661502580019:0.00374067620135064!TCF12#6938;3:10.6344649021864:0.000831352399020207:0.00627987944461676!USF1#7391;3:6.36149927720796:0.0038840405729056:0.0189651369112015!USF2#7392;3:12.9921973850696:0.000455897939342781:0.0042061417744718!YY1#7528;3:4.91117074985386:0.00844145534180826:0.0328177916335286!ZEB1#6935;3:16.8884320175439:0.000207548691732758:0.00242164873375908
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}}
}}

Revision as of 16:00, 26 November 2012


Full id: C3231_lymphangiectasia_Whole_CD4_Neutrophils_CD14_Eosinophils_migratory



Phase1 CAGE Peaks

Hg19::chr12:109027545..109027622,-p1@SELPLG
Hg19::chr12:109027626..109027638,-p3@SELPLG
Hg19::chr12:109027643..109027677,-p2@SELPLG


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 cell8.51e-79168
angioblastic mesenchymal cell8.51e-79168
hematopoietic oligopotent progenitor cell9.32e-76161
hematopoietic multipotent progenitor cell9.32e-76161
hematopoietic cell1.01e-72177
leukocyte4.48e-67136
hematopoietic lineage restricted progenitor cell1.80e-56120
nongranular leukocyte1.25e-54115
myeloid cell1.34e-53108
common myeloid progenitor1.34e-53108
myeloid leukocyte2.26e-4272
granulocyte monocyte progenitor cell1.35e-3667
myeloid lineage restricted progenitor cell2.61e-3666
macrophage dendritic cell progenitor8.04e-3461
monopoietic cell2.47e-3359
monocyte2.47e-3359
monoblast2.47e-3359
promonocyte2.47e-3359
defensive cell6.14e-3148
phagocyte6.14e-3148
classical monocyte6.31e-2742
CD14-positive, CD16-negative classical monocyte6.31e-2742
nucleate cell9.21e-1955
lymphoid lineage restricted progenitor cell1.92e-1852
lymphocyte1.99e-1853
common lymphoid progenitor1.99e-1853
T cell2.33e-1525
pro-T cell2.33e-1525
mature alpha-beta T cell2.10e-1218
alpha-beta T cell2.10e-1218
immature T cell2.10e-1218
mature T cell2.10e-1218
immature alpha-beta T cell2.10e-1218
mesenchymal cell2.62e-11354
connective tissue cell3.49e-10361
stuff accumulating cell2.36e-0987
CD8-positive, alpha-beta T cell2.85e-0811
intermediate monocyte8.82e-089
CD14-positive, CD16-positive monocyte8.82e-089
granulocyte1.77e-078
Uber Anatomy
Ontology termp-valuen
hematopoietic system3.00e-4398
blood island3.00e-4398
hemolymphoid system5.07e-38108
bone marrow7.61e-3176
immune system9.75e-3093
adult organism1.39e-29114
bone element1.30e-2882
skeletal element2.21e-2390
skeletal system1.74e-19100
neural tube2.17e-1056
neural rod2.17e-1056
future spinal cord2.17e-1056
neural keel2.17e-1056
regional part of nervous system2.25e-0953
regional part of brain2.25e-0953
blood3.41e-0915
haemolymphatic fluid3.41e-0915
organism substance3.41e-0915
lateral plate mesoderm4.42e-09203
regional part of forebrain4.81e-0941
forebrain4.81e-0941
anterior neural tube4.81e-0941
future forebrain4.81e-0941
connective tissue5.43e-09371
telencephalon1.13e-0734
brain grey matter1.93e-0734
gray matter1.93e-0734
regional part of telencephalon6.01e-0732
cerebral hemisphere7.81e-0732
Disease
Ontology termp-valuen
leukemia3.09e-1239
hematologic cancer1.07e-1151
immune system cancer1.07e-1151
myeloid leukemia3.38e-1031


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-050.000776777264370707
BCL3#602334.54710280373832.42397750207122e-050.000526534497376906
CHD2#1106310.34402283411690.0009033701102746880.0065875625573927
CTCF#1066435.360256373075030.0064925092527670.0278537287976394
EBF1#187938.9064668465690.00141523283560980.00912774051245923
EGR1#195834.988179094810140.008056488137383440.0319321276880527
ELF1#199734.258097958807540.01295179875054610.0460390357614881
GATA1#2623313.56030814380040.0004009615963782630.00387024289871991
IRF4#3662321.91451268674419.49854535978121e-050.00136210157741342
MAX#414936.452555509007120.003721913834265510.018591589771229
MYC#460935.22228187160940.007020843755740150.0293405586413407
NFKB1#479035.488063424193840.006049381815655430.0268755907540088
PAX5#507936.669565531177830.003370290999677260.0172434145747952
POU2F2#545239.106124057742520.001324165192682130.00879959840662566
SP1#666735.69838137814090.005403962701712170.0245619488469021
SPI1#668838.204323508522730.001810593189410520.0108845071149971
SRF#6722313.79717826216780.0003806615025800190.00374067620135064
TCF12#6938310.63446490218640.0008313523990202070.00627987944461676
USF1#739136.361499277207960.00388404057290560.0189651369112015
USF2#7392312.99219738506960.0004558979393427810.0042061417744718
YY1#752834.911170749853860.008441455341808260.0328177916335286
ZEB1#6935316.88843201754390.0002075486917327580.00242164873375908



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.