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Coexpression cluster:C3119: Difference between revisions

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|tf_chipseq_enrich=CCNT2#905;3:6.33620157696263:0.00393075003576489:0.0189172666229782!CEBPB#1051;3:7.97114762582482:0.00197418705528856:0.0114941532984325!CTCF#10664;3:5.36025637307503:0.006492509252767:0.0278331489142818!E2F1#1869;3:4.90738921487932:0.00846098534723939:0.03236482616124!E2F4#1874;3:12.6680603152844:0.000491798700629898:0.0043550080121321!E2F6#1876;3:5.01715573169739:0.0079176980688633:0.0320460575342588!EGR1#1958;3:4.98817909481014:0.00805648813738344:0.0319103293605958!ETS1#2113;3:9.72876092220234:0.00108584009258484:0.0075997891321182!HMGN3#9324;3:8.17854772335059:0.00182776694216421:0.0108312614430713!JUND#3727;3:6.99466394187103:0.00292184504273499:0.0156177171000665!MAX#4149;3:6.45255550900712:0.00372191383426551:0.0185773733003659!SETDB1#9869;3:40.3200261780105:1.52461559299059e-05:0.000358060103252405!SIN3A#25942;3:5.40888472681514:0.00631896197799152:0.027547108152918!TFAP2C#7022;3:10.8092286098602:0.000791674657575313:0.00613047449859184!THAP1#55145;3:31.3691446028513:3.23800758564397e-05:0.000645001476706219!YY1#7528;3:4.91117074985386:0.00844145534180826:0.0327982572337468!ZBTB7A#51341;3:7.3519093078759:0.00251625586028227:0.0139613900967975
|tf_chipseq_enrich=CCNT2#905;3:6.33620157696263:0.00393075003576489:0.0189172666229782!CEBPB#1051;3:7.97114762582482:0.00197418705528856:0.0114941532984325!CTCF#10664;3:5.36025637307503:0.006492509252767:0.0278331489142818!E2F1#1869;3:4.90738921487932:0.00846098534723939:0.03236482616124!E2F4#1874;3:12.6680603152844:0.000491798700629898:0.0043550080121321!E2F6#1876;3:5.01715573169739:0.0079176980688633:0.0320460575342588!EGR1#1958;3:4.98817909481014:0.00805648813738344:0.0319103293605958!ETS1#2113;3:9.72876092220234:0.00108584009258484:0.0075997891321182!HMGN3#9324;3:8.17854772335059:0.00182776694216421:0.0108312614430713!JUND#3727;3:6.99466394187103:0.00292184504273499:0.0156177171000665!MAX#4149;3:6.45255550900712:0.00372191383426551:0.0185773733003659!SETDB1#9869;3:40.3200261780105:1.52461559299059e-05:0.000358060103252405!SIN3A#25942;3:5.40888472681514:0.00631896197799152:0.027547108152918!TFAP2C#7022;3:10.8092286098602:0.000791674657575313:0.00613047449859184!THAP1#55145;3:31.3691446028513:3.23800758564397e-05:0.000645001476706219!YY1#7528;3:4.91117074985386:0.00844145534180826:0.0327982572337468!ZBTB7A#51341;3:7.3519093078759:0.00251625586028227:0.0139613900967975
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}}
}}

Revision as of 15:56, 26 November 2012


Full id: C3119_CD4_mature_CD8_Neutrophils_Eosinophils_Natural_granulocyte



Phase1 CAGE Peaks

Hg19::chr11:14665263..14665274,+p5@PDE3B
Hg19::chr11:14665275..14665316,+p2@PDE3B
Hg19::chr11:14665329..14665356,+p1@PDE3B


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
hematopoietic stem cell1.56e-31168
angioblastic mesenchymal cell1.56e-31168
hematopoietic oligopotent progenitor cell4.04e-29161
hematopoietic multipotent progenitor cell4.04e-29161
hematopoietic cell3.83e-27177
leukocyte1.81e-25136
nongranular leukocyte1.52e-23115
myeloid cell4.57e-21108
common myeloid progenitor4.57e-21108
hematopoietic lineage restricted progenitor cell3.41e-19120
myeloid leukocyte1.27e-1672
monopoietic cell3.75e-1559
monocyte3.75e-1559
monoblast3.75e-1559
promonocyte3.75e-1559
macrophage dendritic cell progenitor3.53e-1461
myeloid lineage restricted progenitor cell4.35e-1366
defensive cell4.78e-1348
phagocyte4.78e-1348
granulocyte monocyte progenitor cell2.66e-1267
classical monocyte1.14e-1142
CD14-positive, CD16-negative classical monocyte1.14e-1142
stuff accumulating cell9.56e-1187
mature alpha-beta T cell1.15e-1018
alpha-beta T cell1.15e-1018
immature T cell1.15e-1018
mature T cell1.15e-1018
immature alpha-beta T cell1.15e-1018
T cell1.72e-1025
pro-T cell1.72e-1025
CD8-positive, alpha-beta T cell3.35e-0811
nucleate cell3.52e-0855
lymphocyte9.19e-0853
common lymphoid progenitor9.19e-0853
lymphoid lineage restricted progenitor cell1.56e-0752
Uber Anatomy
Ontology termp-valuen
adult organism5.25e-17114
hematopoietic system9.14e-1498
blood island9.14e-1498
hemolymphoid system4.92e-11108
bone marrow1.26e-0876
immune system2.40e-0793
bone element6.35e-0782


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
CCNT2#90536.336201576962630.003930750035764890.0189172666229782
CEBPB#105137.971147625824820.001974187055288560.0114941532984325
CTCF#1066435.360256373075030.0064925092527670.0278331489142818
E2F1#186934.907389214879320.008460985347239390.03236482616124
E2F4#1874312.66806031528440.0004917987006298980.0043550080121321
E2F6#187635.017155731697390.00791769806886330.0320460575342588
EGR1#195834.988179094810140.008056488137383440.0319103293605958
ETS1#211339.728760922202340.001085840092584840.0075997891321182
HMGN3#932438.178547723350590.001827766942164210.0108312614430713
JUND#372736.994663941871030.002921845042734990.0156177171000665
MAX#414936.452555509007120.003721913834265510.0185773733003659
SETDB1#9869340.32002617801051.52461559299059e-050.000358060103252405
SIN3A#2594235.408884726815140.006318961977991520.027547108152918
TFAP2C#7022310.80922860986020.0007916746575753130.00613047449859184
THAP1#55145331.36914460285133.23800758564397e-050.000645001476706219
YY1#752834.911170749853860.008441455341808260.0327982572337468
ZBTB7A#5134137.35190930787590.002516255860282270.0139613900967975



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.

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