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Difference between revisions of "Coexpression cluster:C2877"

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|tf_chipseq_enrich=BATF#10538;4:24.3578017923036:2.83869198020713e-06:9.79419067462348e-05!BCL11A#53335;4:28.3694551036071:1.542446414682e-06:5.90728130190589e-05!BCL3#602;4:34.5471028037383:7.01262157705428e-07:3.15413946979316e-05!BCLAF1#9774;4:21.6526476101218:4.54636978835329e-06:0.000141863852502489!EBF1#1879;4:8.906466846569:0.0001588790747201:0.00200038236102381!EP300#2033;4:6.7739417262232:0.000474845982144264:0.0043525047857789!IRF4#3662;4:21.9145126867441:4.33289161192893e-06:0.000136672566311763!JUND#3727;4:6.99466394187103:0.00041768421781858:0.00392606624289035!MAX#4149;4:6.45255550900712:0.000576761319564549:0.00486483406994039!MEF2A#4205;4:18.7432309096441:8.0978922767748e-06:0.000224690693808205!MEF2C#4208;4:41.3113544926241:3.42889182145094e-07:1.70042750684005e-05!NFKB1#4790;4:5.48806342419384:0.00110219956630198:0.00769212298730453!PAX5#5079;4:6.66956553117783:0.000505277416948326:0.00444909098294125!PBX3#5090;4:21.9145126867441:4.33289161192893e-06:0.000136713857117295!POU2F2#5452;4:9.10612405774252:0.00014539566517493:0.00188773966623626!SIN3A#25942;4:5.40888472681514:0.00116817238488516:0.00798081740727552!SRF#6722;4:13.7971782621678:2.75840773062708e-05:0.000585658355314009!TAF1#6872;4:3.34304628574529:0.00800566489870165:0.0323306769403929!TBP#6908;4:3.70677068709639:0.00529637781478435:0.0245005272001711!TCF12#6938;4:10.6344649021864:7.8163066689251e-05:0.00120278068689534!YY1#7528;4:4.91117074985386:0.0017187183805544:0.0107081804537804
 
|tf_chipseq_enrich=BATF#10538;4:24.3578017923036:2.83869198020713e-06:9.79419067462348e-05!BCL11A#53335;4:28.3694551036071:1.542446414682e-06:5.90728130190589e-05!BCL3#602;4:34.5471028037383:7.01262157705428e-07:3.15413946979316e-05!BCLAF1#9774;4:21.6526476101218:4.54636978835329e-06:0.000141863852502489!EBF1#1879;4:8.906466846569:0.0001588790747201:0.00200038236102381!EP300#2033;4:6.7739417262232:0.000474845982144264:0.0043525047857789!IRF4#3662;4:21.9145126867441:4.33289161192893e-06:0.000136672566311763!JUND#3727;4:6.99466394187103:0.00041768421781858:0.00392606624289035!MAX#4149;4:6.45255550900712:0.000576761319564549:0.00486483406994039!MEF2A#4205;4:18.7432309096441:8.0978922767748e-06:0.000224690693808205!MEF2C#4208;4:41.3113544926241:3.42889182145094e-07:1.70042750684005e-05!NFKB1#4790;4:5.48806342419384:0.00110219956630198:0.00769212298730453!PAX5#5079;4:6.66956553117783:0.000505277416948326:0.00444909098294125!PBX3#5090;4:21.9145126867441:4.33289161192893e-06:0.000136713857117295!POU2F2#5452;4:9.10612405774252:0.00014539566517493:0.00188773966623626!SIN3A#25942;4:5.40888472681514:0.00116817238488516:0.00798081740727552!SRF#6722;4:13.7971782621678:2.75840773062708e-05:0.000585658355314009!TAF1#6872;4:3.34304628574529:0.00800566489870165:0.0323306769403929!TBP#6908;4:3.70677068709639:0.00529637781478435:0.0245005272001711!TCF12#6938;4:10.6344649021864:7.8163066689251e-05:0.00120278068689534!YY1#7528;4:4.91117074985386:0.0017187183805544:0.0107081804537804
 
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 +
|tfbs_overrepresentation_for_novel_motifs=0.590005,1.03954,0.581696,1.75588,0.534346,0.739643,0.821651,0.395818,0.392841,0.151681,0.706765,0.867962,0.905351,0.809319,1.31925,0.559384,1.05593,0.471262,0.356737,0.635753,1.42279,0.169357,0.731221,0.528529,0.632849,0.892087,0.316693,0.728867,0.537869,0.297585,1.63433,1.09415,0.433165,0.344471,0.49475,0.0842336,0.491074,0.740899,0.463978,0.371755,0.493145,0.66492,0.183156,2.26333,0.0946706,0.61613,0.822818,0.694903,0.515703,0.538016,0.90714,0.83543,0.25073,1.17354,1.33024,0.812467,0.54284,0.777235,0.297448,0.776148,1.13655,0.825354,0.393426,1.02706,0.844545,0.991076,1.42026,1.79268,1.08337,1.62905,0.650393,0.402607,0.248021,1.32819,0.336329,0.321165,0.823598,1.00941,1.08,1.51572,0.362435,1.02594,0.844168,0.399165,1.27559,0.109222,0.6318,0.291738,0.934646,1.89266,1.51507,1.24792,1.11156,0.441618,0.535192,2.0177,0.354969,1.15558,0.939507,2.11025,0.465545,1.1057,1.14983,1.05974,0.979006,0.701817,1.04326,0.805616,0.632569,0.516141,0.594299,1.14697,0.575476,1.70537,1.46636,0.489254,0.12452,0.681522,0.988625,1.1313,1.31973,0.932085,0.736652,0.856196,1.57854,1.0102,1.90732,1.11673,1.36323,0.458105,2.78996,0.68598,1.37788,0.852645,1.52813,0.283547,0.676268,0.729481,1.48509,2.34913,1.94535,1.44718,0.8167,1.15194,0.980848,0.768101,0.963351,2.1895,0.661255,1.11576,0.234974,0.175846,1.24902,0.383416,0.824835,1.65997,3.48962,0.518428,0.632914,0.600782,1.44595,1.23002,1.07918,0.604379,0.997702,0.843324,1.90479,0.820225,0.359498
 
}}
 
}}

Revision as of 06:47, 26 November 2012


Full id: C2877_CD14_Eosinophils_neuroectodermal_CD8_cord_CD4_Natural



Phase1 CAGE Peaks

  Short description
Hg19::chr7:130645970..130645981,- p@chr7:130645970..130645981
-
Hg19::chr7:130645982..130645997,- p@chr7:130645982..130645997
-
Hg19::chr7:130645999..130646023,- p@chr7:130645999..130646023
-
Hg19::chr7:130646084..130646098,- p@chr7:130646084..130646098
-


Enriched pathways on this co-expression clusterSummary:
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.
Analyst: Emmanuel Dimont

link to source dataset
data


No results for this coexpression

Enriched Gene Ontology terms on this co-expression clusterSummary: 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.
Analyst: Erik Arner

link to source dataset
data


No GOStat results

Enriched sample ontology terms on this co-expression clusterSummary: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. Analyst: Hideya Kawaji

links to source dataset

cell_data
uberon_data


Cell Type
Ontology termp-valuen
leukocyte6.88e-34136
nongranular leukocyte2.58e-30115
hematopoietic stem cell1.95e-28168
angioblastic mesenchymal cell1.95e-28168
hematopoietic cell3.70e-28177
hematopoietic oligopotent progenitor cell3.03e-27161
hematopoietic multipotent progenitor cell3.03e-27161
hematopoietic lineage restricted progenitor cell4.43e-24120
classical monocyte1.06e-1942
CD14-positive, CD16-negative classical monocyte1.06e-1942
defensive cell3.34e-1648
phagocyte3.34e-1648
mesenchymal cell1.20e-15354
lymphocyte1.69e-1553
common lymphoid progenitor1.69e-1553
motile cell2.83e-15386
lymphoid lineage restricted progenitor cell3.48e-1552
myeloid leukocyte5.28e-1572
nucleate cell3.27e-1455
connective tissue cell3.85e-14361
monopoietic cell2.67e-1359
monocyte2.67e-1359
monoblast2.67e-1359
promonocyte2.67e-1359
macrophage dendritic cell progenitor3.78e-1361
myeloid cell1.65e-12108
common myeloid progenitor1.65e-12108
T cell4.14e-1125
pro-T cell4.14e-1125
granulocyte monocyte progenitor cell2.70e-1067
myeloid lineage restricted progenitor cell6.04e-1066
mature alpha-beta T cell7.96e-1018
alpha-beta T cell7.96e-1018
immature T cell7.96e-1018
mature T cell7.96e-1018
immature alpha-beta T cell7.96e-1018
native cell2.30e-09722
multi fate stem cell3.70e-09427
somatic stem cell4.39e-09433
stem cell1.25e-08441
granulocyte5.79e-078
animal cell7.43e-07679
eukaryotic cell7.43e-07679
Uber Anatomy
Ontology termp-valuen
connective tissue2.54e-15371
hematopoietic system2.97e-1298
blood island2.97e-1298
bone element3.07e-1182
bone marrow2.12e-1076
skeletal element2.44e-1090
skeletal system3.05e-10100
hemolymphoid system1.93e-09108
immune system8.41e-0993


Overrepresented TFBS (DNA) motifs on this co-expression clusterSummary: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. Analyst: Michiel de Hoon

link to source data
Novel motifs
data

Jaspar motifs
data


Novel motifs



JASPAR motifs

Motifs-log10(p-value)

{{{tfbs_overrepresentation_jaspar}}}



ENCODE TF ChIP-seq peak enrichment analysisSummary: 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.
Analyst: Erik Arner

link to source dataset

data


(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
BATF#10538424.35780179230362.83869198020713e-069.79419067462348e-05
BCL11A#53335428.36945510360711.542446414682e-065.90728130190589e-05
BCL3#602434.54710280373837.01262157705428e-073.15413946979316e-05
BCLAF1#9774421.65264761012184.54636978835329e-060.000141863852502489
EBF1#187948.9064668465690.00015887907472010.00200038236102381
EP300#203346.77394172622320.0004748459821442640.0043525047857789
IRF4#3662421.91451268674414.33289161192893e-060.000136672566311763
JUND#372746.994663941871030.000417684217818580.00392606624289035
MAX#414946.452555509007120.0005767613195645490.00486483406994039
MEF2A#4205418.74323090964418.0978922767748e-060.000224690693808205
MEF2C#4208441.31135449262413.42889182145094e-071.70042750684005e-05
NFKB1#479045.488063424193840.001102199566301980.00769212298730453
PAX5#507946.669565531177830.0005052774169483260.00444909098294125
PBX3#5090421.91451268674414.33289161192893e-060.000136713857117295
POU2F2#545249.106124057742520.000145395665174930.00188773966623626
SIN3A#2594245.408884726815140.001168172384885160.00798081740727552
SRF#6722413.79717826216782.75840773062708e-050.000585658355314009
TAF1#687243.343046285745290.008005664898701650.0323306769403929
TBP#690843.706770687096390.005296377814784350.0245005272001711
TCF12#6938410.63446490218647.8163066689251e-050.00120278068689534
YY1#752844.911170749853860.00171871838055440.0107081804537804



Relative expression of the co-expression clusterSummary:Co-expression clusters are compared against FANTOM5 samples to obtain relative expression.
Analyst:NA

link to data source
data


This analysis result is provided for C0 - C305 clusters.