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Coexpression cluster:C654: Difference between revisions

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|tf_chipseq_enrich=BCL11A#53335;6:13.0935946632033:2.65123192532282e-06:9.29167822311376e-05!CTCF#10664;7:2.88629189319425:0.00467512780428698:0.022060528294941!EBF1#1879;10:6.85112834351462:6.58271412928801e-08:4.02512927955919e-06!ELF1#1997;9:2.94791397148214:0.000603403467917953:0.00503989561627344!GABPB1#2553;6:3.26200792439177:0.00561630441383157:0.0253944591166402!IRF4#3662;5:8.42865872567082:0.000186792261757661:0.00225974713607186!MAX#4149;6:2.97810254261867:0.00885876695823828:0.0336155492624877!NFKB1#4790;11:4.64374597431786:3.97495193507342e-07:1.92551022795516e-05!PAX5#5079;6:3.07826101438977:0.00751515295554873:0.0309884341252588!POLR2A#5430;13:2.14745317655807:4.83928878402115e-05:0.000840809318440167!POU2F2#5452;5:3.50235540682405:0.00961613860265682:0.0361896832374644!SP1#6667;7:3.06835920361433:0.00326017741207416:0.0168860180886537!SPI1#6688;7:4.41771265843531:0.000349608792469154:0.00352951113356076!SRF#6722;5:5.3066070239107:0.00156826497609789:0.00994764809223732!TAF1#6872;10:2.57157406595792:0.000635041234822482:0.0052112101456451!TBP#6908;11:3.13649827369694:2.43452380190334e-05:0.000528166247085547!TCF12#6938;8:6.54428609365318:5.08413564000193e-06:0.000156724333561441!USF1#7391;6:2.9360765894806:0.00950376317872054:0.0358003073984633!USF2#7392;4:3.99759919540603:0.0142546073921536:0.049996203157777
|tf_chipseq_enrich=BCL11A#53335;6:13.0935946632033:2.65123192532282e-06:9.29167822311376e-05!CTCF#10664;7:2.88629189319425:0.00467512780428698:0.022060528294941!EBF1#1879;10:6.85112834351462:6.58271412928801e-08:4.02512927955919e-06!ELF1#1997;9:2.94791397148214:0.000603403467917953:0.00503989561627344!GABPB1#2553;6:3.26200792439177:0.00561630441383157:0.0253944591166402!IRF4#3662;5:8.42865872567082:0.000186792261757661:0.00225974713607186!MAX#4149;6:2.97810254261867:0.00885876695823828:0.0336155492624877!NFKB1#4790;11:4.64374597431786:3.97495193507342e-07:1.92551022795516e-05!PAX5#5079;6:3.07826101438977:0.00751515295554873:0.0309884341252588!POLR2A#5430;13:2.14745317655807:4.83928878402115e-05:0.000840809318440167!POU2F2#5452;5:3.50235540682405:0.00961613860265682:0.0361896832374644!SP1#6667;7:3.06835920361433:0.00326017741207416:0.0168860180886537!SPI1#6688;7:4.41771265843531:0.000349608792469154:0.00352951113356076!SRF#6722;5:5.3066070239107:0.00156826497609789:0.00994764809223732!TAF1#6872;10:2.57157406595792:0.000635041234822482:0.0052112101456451!TBP#6908;11:3.13649827369694:2.43452380190334e-05:0.000528166247085547!TCF12#6938;8:6.54428609365318:5.08413564000193e-06:0.000156724333561441!USF1#7391;6:2.9360765894806:0.00950376317872054:0.0358003073984633!USF2#7392;4:3.99759919540603:0.0142546073921536:0.049996203157777
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|tfbs_overrepresentation_for_novel_motifs=0.208137,0.981855,0.202418,0.320418,0.17087,0.319017,0.385011,0.628761,1.04054,0.251333,0.293498,0.423573,0.499876,0.37489,0.506988,0.549464,0.587543,0.412009,0.250662,0.74987,0.202464,0.300734,0.312425,0.167123,0.238419,0.443987,0.772359,0.310589,0.173154,0.399779,0.755662,0.622056,0.721119,0.234859,0.145955,0.928315,0.442053,0.320003,0.127608,0.570628,0.144976,0.261903,0.340762,0.16875,0.360234,0.642555,0.385972,1.41723,0.312409,0.515273,0.456831,0.396393,0.551018,0.694739,0.841347,0.377467,0.176395,0.348876,0.706527,0.348003,0.660716,0.388062,0.62293,0.561703,0.403967,0.529794,0.927044,1.28869,0.612294,1.12869,0.700198,1.07567,0.294551,0.839414,0.224555,1.20069,0.186653,0.546008,0.609242,0.659074,0.548433,0.560705,0.403653,1.06327,0.789807,0.268154,0.0982734,0.687175,0.480498,1.38705,1.01818,0.763867,0.637885,0.114875,0.984035,0.123575,0.248364,0.67819,1.21675,0.972854,0.403442,0.632556,0.672898,0.590971,0.519171,0.289709,0.576179,0.371864,0.670087,0.15924,0.606372,0.670274,0.198172,0.814965,0.971251,0.439271,0.767357,0.753394,0.527634,0.116746,0.831412,0.478284,0.316671,0.413695,1.0796,0.546713,0.379419,0.642598,0.872646,0.124214,0.76453,0.277675,0.886589,1.86125,1.03079,1.02457,0.270369,0.836727,0.989273,1.83943,1.43902,0.95284,0.38094,0.674844,0.52079,0.341558,0.505455,1.68078,0.259186,0.362523,0.110712,0.159485,0.764896,0.0843101,0.387634,1.15881,0.465765,0.160686,0.238466,0.617071,0.951654,0.747146,0.608503,0.623024,0.535644,0.402951,0.341994,0.383837,1.23381
}}
}}

Revision as of 14:22, 26 November 2012


Full id: C654_Eosinophils_Neutrophils_Natural_CD8_CD4_CD14_CD34



Phase1 CAGE Peaks

Hg19::chr11:269478..269491,-p@chr11:269478..269491
-
Hg19::chr17:40440375..40440398,-p@chr17:40440375..40440398
-
Hg19::chr17:47817223..47817245,+p@chr17:47817223..47817245
+
Hg19::chr17:7747301..7747312,-p@chr17:7747301..7747312
-
Hg19::chr19:13948014..13948028,+p@chr19:13948014..13948028
+
Hg19::chr2:43386231..43386235,+p@chr2:43386231..43386235
+
Hg19::chr2:70313762..70313774,-p18@PCBP1-AS1
Hg19::chr3:196438771..196438791,-p@chr3:196438771..196438791
-
Hg19::chr4:123073610..123073629,+p2@KIAA1109
Hg19::chr5:131763102..131763114,-p@chr5:131763102..131763114
-
Hg19::chr9:117135390..117135416,-p@chr9:117135390..117135416
-
Hg19::chr9:117145466..117145492,+p@chr9:117145466..117145492
+
Hg19::chr9:117147710..117147721,-p@chr9:117147710..117147721
-


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


GO IDGO nameFDR corrected p-value
GO:0004190aspartic-type endopeptidase activity0.0275226657247145



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
leukocyte3.63e-67136
hematopoietic stem cell3.81e-52168
angioblastic mesenchymal cell3.81e-52168
hematopoietic lineage restricted progenitor cell4.68e-50120
hematopoietic cell5.15e-50177
nongranular leukocyte1.62e-49115
hematopoietic oligopotent progenitor cell7.12e-48161
hematopoietic multipotent progenitor cell7.12e-48161
myeloid leukocyte4.96e-3972
classical monocyte7.38e-3642
CD14-positive, CD16-negative classical monocyte7.38e-3642
defensive cell3.23e-3048
phagocyte3.23e-3048
granulocyte monocyte progenitor cell1.35e-2867
macrophage dendritic cell progenitor1.27e-2661
myeloid cell4.93e-26108
common myeloid progenitor4.93e-26108
myeloid lineage restricted progenitor cell1.77e-2566
mature alpha-beta T cell1.89e-2418
alpha-beta T cell1.89e-2418
immature T cell1.89e-2418
mature T cell1.89e-2418
immature alpha-beta T cell1.89e-2418
monopoietic cell4.74e-2459
monocyte4.74e-2459
monoblast4.74e-2459
promonocyte4.74e-2459
lymphoid lineage restricted progenitor cell1.39e-2052
lymphocyte4.77e-2053
common lymphoid progenitor4.77e-2053
nucleate cell4.90e-1955
T cell1.78e-1825
pro-T cell1.78e-1825
granulocyte3.82e-188
intermediate monocyte1.14e-169
CD14-positive, CD16-positive monocyte1.14e-169
blood cell1.45e-1511
CD8-positive, alpha-beta T cell1.56e-1411
mesenchymal cell2.34e-14354
connective tissue cell1.03e-13361
CD4-positive, alpha-beta T cell1.13e-136
stuff accumulating cell8.72e-1387
motile cell1.86e-11386
multi fate stem cell9.38e-09427
stem cell1.84e-08441
somatic stem cell2.18e-08433
neutrophil4.27e-083
natural killer cell4.36e-083
pro-NK cell4.36e-083
naive T cell1.49e-073
basophil1.81e-073
single nucleate cell2.15e-073
mononuclear cell2.15e-073
Uber Anatomy
Ontology termp-valuen
hematopoietic system7.40e-3898
blood island7.40e-3898
hemolymphoid system1.58e-34108
bone marrow5.26e-2476
immune system5.90e-2393
bone element1.64e-2182
skeletal element1.03e-1890
skeletal system7.29e-16100
blood8.10e-1515
haemolymphatic fluid8.10e-1515
organism substance8.10e-1515
connective tissue7.78e-13371
lateral plate mesoderm2.70e-11203


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#53335613.09359466320332.65123192532282e-069.29167822311376e-05
CTCF#1066472.886291893194250.004675127804286980.022060528294941
EBF1#1879106.851128343514626.58271412928801e-084.02512927955919e-06
ELF1#199792.947913971482140.0006034034679179530.00503989561627344
GABPB1#255363.262007924391770.005616304413831570.0253944591166402
IRF4#366258.428658725670820.0001867922617576610.00225974713607186
MAX#414962.978102542618670.008858766958238280.0336155492624877
NFKB1#4790114.643745974317863.97495193507342e-071.92551022795516e-05
PAX5#507963.078261014389770.007515152955548730.0309884341252588
POLR2A#5430132.147453176558074.83928878402115e-050.000840809318440167
POU2F2#545253.502355406824050.009616138602656820.0361896832374644
SP1#666773.068359203614330.003260177412074160.0168860180886537
SPI1#668874.417712658435310.0003496087924691540.00352951113356076
SRF#672255.30660702391070.001568264976097890.00994764809223732
TAF1#6872102.571574065957920.0006350412348224820.0052112101456451
TBP#6908113.136498273696942.43452380190334e-050.000528166247085547
TCF12#693886.544286093653185.08413564000193e-060.000156724333561441
USF1#739162.93607658948060.009503763178720540.0358003073984633
USF2#739243.997599195406030.01425460739215360.049996203157777



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.