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Coexpression cluster:C3718: Difference between revisions

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|tf_chipseq_enrich=CCNT2#905;3:6.33620157696263:0.00393075003576489:0.0189907759164199!CHD2#1106;3:10.3440228341169:0.000903370110274688:0.00660139035453248!CTCF#10664;3:5.36025637307503:0.006492509252767:0.0279282991000343!E2F4#1874;3:12.6680603152844:0.000491798700629898:0.00436797044774947!E2F6#1876;3:5.01715573169739:0.0079176980688633:0.0321970357284591!ELF1#1997;3:4.25809795880754:0.0129517987505461:0.0461978452769222!EP300#2033;3:6.7739417262232:0.00321688050010379:0.0167397998281186!FOS#2353;3:8.9979553088944:0.00137249927241713:0.0089712386726732!FOSL2#2355;3:16.9302006045617:0.000206016205317162:0.00242955357578129!GATA1#2623;3:13.5603081438004:0.000400961596378263:0.00387776906789049!GTF2F1#2962;3:12.7396608767577:0.000483552504743859:0.00433677458505315!HDAC2#3066;3:13.4156202366263:0.000414076139985721:0.00391186775069821!HMGN3#9324;3:8.17854772335059:0.00182776694216421:0.0108645504651502!IRF1#3659;3:7.6371637535639:0.00224469274729724:0.0127986824171522!JUN#3725;3:12.5128291923363:0.000510331399272625:0.00444006173014276!JUNB#3726;3:30.6106326598211:3.4847716247536e-05:0.000680273016294657!JUND#3727;3:6.99466394187103:0.00292184504273499:0.0156674320695281!MYC#4609;3:5.2222818716094:0.00702084375574015:0.0294300582382398!NR3C1#2908;3:14.973023331173:0.000297833119467548:0.00308799693875422!PBX3#5090;2:14.6096751244961:0.00605612247321789:0.0268290721094551!SIN3A#25942;3:5.40888472681514:0.00631896197799152:0.0276509854619121!SMC3#9126;3:15.0449328449328:0.000293582542037187:0.00308931658517095!SPI1#6688;3:8.20432350852273:0.00181059318941052:0.0109033351847342!STAT3#6774;3:10.5194649971542:0.000858918453041531:0.00642582982214932!TAL1#6886;3:29.8686166774402:3.75103522793067e-05:0.000719739790868732!TCF12#6938;3:10.6344649021864:0.000831352399020207:0.00629034363553368!TCF7L2#6934;3:10.7701765631373:0.000800318129839838:0.00613328626081177!YY1#7528;3:4.91117074985386:0.00844145534180826:0.0329158137112871!ZNF263#10127;3:8.22184163701068:0.00179904392556587:0.010934664991106
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}}
}}

Revision as of 16:18, 26 November 2012


Full id: C3718_CD14_Mast_Natural_Eosinophils_Basophils_CD8_CD19



Phase1 CAGE Peaks

Hg19::chr18:3448390..3448411,+p14@TGIF1
Hg19::chr18:3448422..3448439,+p11@TGIF1
Hg19::chr18:3448730..3448744,+p@chr18:3448730..3448744
+


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
classical monocyte1.90e-2542
CD14-positive, CD16-negative classical monocyte1.90e-2542
defensive cell6.28e-2348
phagocyte6.28e-2348
myeloid leukocyte7.35e-2372
granulocyte monocyte progenitor cell1.09e-2167
myeloid lineage restricted progenitor cell1.75e-2166
leukocyte1.41e-20136
macrophage dendritic cell progenitor3.76e-2061
monopoietic cell2.69e-1959
monocyte2.69e-1959
monoblast2.69e-1959
promonocyte2.69e-1959
myeloid cell4.81e-19108
common myeloid progenitor4.81e-19108
hematopoietic stem cell3.02e-18168
angioblastic mesenchymal cell3.02e-18168
hematopoietic lineage restricted progenitor cell6.57e-18120
hematopoietic oligopotent progenitor cell6.34e-17161
hematopoietic multipotent progenitor cell6.34e-17161
hematopoietic cell6.42e-16177
nongranular leukocyte8.26e-16115
animal cell5.47e-14679
eukaryotic cell5.47e-14679
native cell1.04e-13722
stem cell3.33e-13441
multi fate stem cell1.25e-12427
mesenchymal cell2.57e-12354
somatic stem cell5.92e-12433
connective tissue cell6.03e-12361
stuff accumulating cell7.60e-1287
motile cell1.28e-10386
somatic cell5.10e-09588
Uber Anatomy
Ontology termp-valuen
bone marrow4.05e-1976
bone element1.04e-1782
skeletal element2.70e-1590
immune system5.91e-1393
hematopoietic system1.94e-1298
blood island1.94e-1298
skeletal system4.25e-12100
connective tissue1.84e-11371
hemolymphoid system1.61e-09108
musculoskeletal system3.02e-08167
lateral plate mesoderm5.38e-08203


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#90536.336201576962630.003930750035764890.0189907759164199
CHD2#1106310.34402283411690.0009033701102746880.00660139035453248
CTCF#1066435.360256373075030.0064925092527670.0279282991000343
E2F4#1874312.66806031528440.0004917987006298980.00436797044774947
E2F6#187635.017155731697390.00791769806886330.0321970357284591
ELF1#199734.258097958807540.01295179875054610.0461978452769222
EP300#203336.77394172622320.003216880500103790.0167397998281186
FOS#235338.99795530889440.001372499272417130.0089712386726732
FOSL2#2355316.93020060456170.0002060162053171620.00242955357578129
GATA1#2623313.56030814380040.0004009615963782630.00387776906789049
GTF2F1#2962312.73966087675770.0004835525047438590.00433677458505315
HDAC2#3066313.41562023662630.0004140761399857210.00391186775069821
HMGN3#932438.178547723350590.001827766942164210.0108645504651502
IRF1#365937.63716375356390.002244692747297240.0127986824171522
JUN#3725312.51282919233630.0005103313992726250.00444006173014276
JUNB#3726330.61063265982113.4847716247536e-050.000680273016294657
JUND#372736.994663941871030.002921845042734990.0156674320695281
MYC#460935.22228187160940.007020843755740150.0294300582382398
NR3C1#2908314.9730233311730.0002978331194675480.00308799693875422
PBX3#5090214.60967512449610.006056122473217890.0268290721094551
SIN3A#2594235.408884726815140.006318961977991520.0276509854619121
SMC3#9126315.04493284493280.0002935825420371870.00308931658517095
SPI1#668838.204323508522730.001810593189410520.0109033351847342
STAT3#6774310.51946499715420.0008589184530415310.00642582982214932
TAL1#6886329.86861667744023.75103522793067e-050.000719739790868732
TCF12#6938310.63446490218640.0008313523990202070.00629034363553368
TCF7L2#6934310.77017656313730.0008003181298398380.00613328626081177
YY1#752834.911170749853860.008441455341808260.0329158137112871
ZNF263#1012738.221841637010680.001799043925565870.010934664991106



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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