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Difference between revisions of "Coexpression cluster:C612"

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|tf_chipseq_enrich=ATF3#467;5:8.02256233071741:0.000249231279312087:0.00268760615178886!CCNT2#905;9:4.07327244233312:5.6650649163175e-05:0.000949380158529018!E2F1#1869;10:3.50527801062809:5.45556518161784e-05:0.000924207253857235!E2F6#1876;11:3.94205093204795:3.91931737261351e-06:0.000127556742623366!EGR1#1958;7:2.49408954740507:0.0117605194461907:0.04285613714029!ELF1#1997;9:2.73734868780485:0.00133657072811265:0.00887018556734812!HEY1#23462;13:3.75153168288387:1.40950819416918e-07:7.98739155132038e-06!HMGN3#9324;8:4.67345584191462:7.53694136401289e-05:0.0011666675842836!JUND#3727;6:2.99771311794473:0.00911646392082055:0.0344931484051218!NFKB1#4790;9:3.52804077269604:0.000181629889293606:0.0022016299916359!NRF1#4899;6:5.23297690616182:0.000507577770393346:0.00444834394244447!POLR2A#5430;14:2.14745317655807:2.25331953374171e-05:0.000492537544546777!POU2F2#5452;5:3.25218716347947:0.0136235155601946:0.0480684574861879!SIX5#147912;4:4.88191867298829:0.00730145528674041:0.0302002648986884!SMC3#9126;4:4.29855224140938:0.0113787067695173:0.0417034235086193!TAF1#6872;12:2.86546824492454:2.44753931259235e-05:0.000530659244898966!TBP#6908;13:3.44200135230379:4.20225918943144e-07:2.02062498842095e-05!USF2#7392;6:5.56808459360125:0.000362490831700241:0.00362071346326908!YY1#7528;12:4.20957492844616:3.04483641911638e-07:1.5325285338607e-05!ZBTB7A#51341;7:3.67595465393795:0.00122472924108481:0.00823734526079707!ZNF143#7702;6:5.78608995095481:0.000293990833817525:0.00306979690992486
 
|tf_chipseq_enrich=ATF3#467;5:8.02256233071741:0.000249231279312087:0.00268760615178886!CCNT2#905;9:4.07327244233312:5.6650649163175e-05:0.000949380158529018!E2F1#1869;10:3.50527801062809:5.45556518161784e-05:0.000924207253857235!E2F6#1876;11:3.94205093204795:3.91931737261351e-06:0.000127556742623366!EGR1#1958;7:2.49408954740507:0.0117605194461907:0.04285613714029!ELF1#1997;9:2.73734868780485:0.00133657072811265:0.00887018556734812!HEY1#23462;13:3.75153168288387:1.40950819416918e-07:7.98739155132038e-06!HMGN3#9324;8:4.67345584191462:7.53694136401289e-05:0.0011666675842836!JUND#3727;6:2.99771311794473:0.00911646392082055:0.0344931484051218!NFKB1#4790;9:3.52804077269604:0.000181629889293606:0.0022016299916359!NRF1#4899;6:5.23297690616182:0.000507577770393346:0.00444834394244447!POLR2A#5430;14:2.14745317655807:2.25331953374171e-05:0.000492537544546777!POU2F2#5452;5:3.25218716347947:0.0136235155601946:0.0480684574861879!SIX5#147912;4:4.88191867298829:0.00730145528674041:0.0302002648986884!SMC3#9126;4:4.29855224140938:0.0113787067695173:0.0417034235086193!TAF1#6872;12:2.86546824492454:2.44753931259235e-05:0.000530659244898966!TBP#6908;13:3.44200135230379:4.20225918943144e-07:2.02062498842095e-05!USF2#7392;6:5.56808459360125:0.000362490831700241:0.00362071346326908!YY1#7528;12:4.20957492844616:3.04483641911638e-07:1.5325285338607e-05!ZBTB7A#51341;7:3.67595465393795:0.00122472924108481:0.00823734526079707!ZNF143#7702;6:5.78608995095481:0.000293990833817525:0.00306979690992486
 
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 +
|tfbs_overrepresentation_for_novel_motifs=2.36567,0.844166,0.541316,0.297884,0.153879,0.296522,0.360887,0.0785261,0.0771434,1.90495,1.37072,0.398649,0.446874,0.350994,0.152923,0.169541,1.37708,0.117033,0.0612687,0.0824773,0.184,0.440546,0.789382,0.150321,0.623871,0.418678,0.0456804,0.288329,1.4739,0.152963,0.254115,0.594213,1.61483,0.205943,0.407984,2.01336,1.88982,0.29748,0.113038,2.41888,0.40562,1.25681,0.142503,0.151865,2.63051,0.596593,0.949837,0.262957,0.127784,0.15614,0.431291,0.372023,0.485552,0.666176,0.811691,0.353512,0.15913,0.325599,0.0389839,0.324748,1.52924,0.363871,0.0774141,1.32304,0.988629,0.503101,0.896916,1.25738,0.584559,1.09778,0.230809,0.278952,4.92396,0.80977,3.38061,0.402042,0.16121,0.519091,0.581542,0.213774,0.227702,1.32095,0.37913,0.0800936,0.760489,8.66872,0.973972,2.94,0.454557,1.35556,0.98765,0.734737,0.609873,0.101133,3.58574,0.109261,0.218567,0.649779,2.02341,0.301239,0.113893,0.6046,0.644537,0.563483,1.23371,2.08808,0.548871,0.348037,1.16972,1.39424,0.561401,0.641937,0.531469,0.279418,0.940917,0.12714,1.22572,0.253155,0.500972,0.102878,0.801818,0.452379,0.294241,0.388967,1.04884,0.519787,0.355419,0.614537,0.842806,0.109858,0.735394,0.712269,0.856671,1.00316,1.00021,0.925323,0.249339,0.288795,0.95886,1.80749,1.40745,0.922589,0.356906,0.646464,1.23712,0.853342,0.47912,1.64894,0.238532,0.66991,1.43996,9.00473,0.735758,0.921167,0.363452,1.12781,0.440071,0.443316,0.218554,1.70713,0.921409,0.718143,0.580811,0.577588,0.508869,0.378443,0.635551,0.35974,5.48661
 
}}
 
}}

Revision as of 05:21, 26 November 2012


Full id: C612_Neutrophils_Eosinophils_granulocyte_CD14_CD4_acute_CD19



Phase1 CAGE Peaks

  Short description
Hg19::chr10:114206956..114207040,+ p1@VTI1A
Hg19::chr10:30024802..30024871,- p5@SVIL
Hg19::chr12:116715340..116715396,- p2@MED13L
Hg19::chr12:116715402..116715427,- p3@MED13L
Hg19::chr13:28712614..28712703,+ p2@PAN3
Hg19::chr14:51297837..51297887,- p1@NIN
Hg19::chr17:4046257..4046349,- p1@ZZEF1
Hg19::chr17:63052873..63052927,- p2@GNA13
Hg19::chr1:16174280..16174365,+ p1@SPEN
Hg19::chr20:20693269..20693316,- p1@RALGAPA2
Hg19::chr22:24059505..24059562,- p1@GUSBP11
Hg19::chr3:57678772..57678838,- p1@FAM116A
Hg19::chr6:79787593..79787644,- p@chr6:79787593..79787644
-
Hg19::chr7:152133059..152133102,- p1@MLL3


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
leukocyte9.07e-47136
hematopoietic stem cell4.66e-46168
angioblastic mesenchymal cell4.66e-46168
hematopoietic oligopotent progenitor cell5.60e-42161
hematopoietic multipotent progenitor cell5.60e-42161
hematopoietic cell8.09e-41177
hematopoietic lineage restricted progenitor cell1.81e-36120
nongranular leukocyte2.39e-35115
myeloid leukocyte3.81e-2872
myeloid cell4.14e-28108
common myeloid progenitor4.14e-28108
granulocyte monocyte progenitor cell8.05e-2567
myeloid lineage restricted progenitor cell1.26e-2266
macrophage dendritic cell progenitor2.42e-2261
monopoietic cell2.95e-2159
monocyte2.95e-2159
monoblast2.95e-2159
promonocyte2.95e-2159
classical monocyte5.37e-2142
CD14-positive, CD16-negative classical monocyte5.37e-2142
defensive cell2.47e-2048
phagocyte2.47e-2048
lymphoid lineage restricted progenitor cell1.47e-1252
lymphocyte2.44e-1253
common lymphoid progenitor2.44e-1253
nucleate cell4.33e-1255
mature alpha-beta T cell3.46e-0918
alpha-beta T cell3.46e-0918
immature T cell3.46e-0918
mature T cell3.46e-0918
immature alpha-beta T cell3.46e-0918
T cell1.73e-0725
pro-T cell1.73e-0725
Uber Anatomy
Ontology termp-valuen
hematopoietic system1.36e-2798
blood island1.36e-2798
hemolymphoid system6.28e-25108
adult organism8.00e-22114
bone marrow4.15e-1976
immune system6.22e-1993
bone element2.54e-1882
skeletal element1.31e-1390
skeletal system2.84e-11100
blood2.19e-0715
haemolymphatic fluid2.19e-0715
organism substance2.19e-0715
neural tube3.22e-0756
neural rod3.22e-0756
future spinal cord3.22e-0756
neural keel3.22e-0756


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
ATF3#46758.022562330717410.0002492312793120870.00268760615178886
CCNT2#90594.073272442333125.6650649163175e-050.000949380158529018
E2F1#1869103.505278010628095.45556518161784e-050.000924207253857235
E2F6#1876113.942050932047953.91931737261351e-060.000127556742623366
EGR1#195872.494089547405070.01176051944619070.04285613714029
ELF1#199792.737348687804850.001336570728112650.00887018556734812
HEY1#23462133.751531682883871.40950819416918e-077.98739155132038e-06
HMGN3#932484.673455841914627.53694136401289e-050.0011666675842836
JUND#372762.997713117944730.009116463920820550.0344931484051218
NFKB1#479093.528040772696040.0001816298892936060.0022016299916359
NRF1#489965.232976906161820.0005075777703933460.00444834394244447
POLR2A#5430142.147453176558072.25331953374171e-050.000492537544546777
POU2F2#545253.252187163479470.01362351556019460.0480684574861879
SIX5#14791244.881918672988290.007301455286740410.0302002648986884
SMC3#912644.298552241409380.01137870676951730.0417034235086193
TAF1#6872122.865468244924542.44753931259235e-050.000530659244898966
TBP#6908133.442001352303794.20225918943144e-072.02062498842095e-05
USF2#739265.568084593601250.0003624908317002410.00362071346326908
YY1#7528124.209574928446163.04483641911638e-071.5325285338607e-05
ZBTB7A#5134173.675954653937950.001224729241084810.00823734526079707
ZNF143#770265.786089950954810.0002939908338175250.00306979690992486



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.