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Coexpression cluster:C654: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002390!1.84e-26!102;UBERON:0003061!1.84e-26!102;UBERON:0002193!9.43e-24!112;UBERON:0002371!6.92e-18!80;UBERON:0001474!1.63e-15!86;UBERON:0007023!1.70e-14!115;UBERON:0002405!1.74e-14!115;UBERON:0004765!1.38e-11!101;UBERON:0001434!1.38e-11!101;UBERON:0002384!1.86e-08!375;UBERON:0000178!3.65e-08!15;UBERON:0000179!3.65e-08!15;UBERON:0000463!3.65e-08!15
|ontology_enrichment_uberon=UBERON:0002390!1.84e-26!102;UBERON:0003061!1.84e-26!102;UBERON:0002193!9.43e-24!112;UBERON:0002371!6.92e-18!80;UBERON:0001474!1.63e-15!86;UBERON:0007023!1.70e-14!115;UBERON:0002405!1.74e-14!115;UBERON:0004765!1.38e-11!101;UBERON:0001434!1.38e-11!101;UBERON:0002384!1.86e-08!375;UBERON:0000178!3.65e-08!15;UBERON:0000179!3.65e-08!15;UBERON:0000463!3.65e-08!15
|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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.157864,0.720209,0.194458,0.621884,0.195258,0.565342,0.324691,0.135616,0.285075,0.65843,0.160125,0.233943,0.211923,0.432296,0.393162,0.396542,0.145945,0.118166,0.453406,0.491678,0.157767,0.327371,0.217504,0.490389,0.135586,0.653686,0.598834,0.456047,0.369487,0.0314515,0.430658,0.290434,0.559767,0.309388,0.0586843,0.829367,0.499692,0.483637,0.18876,0.481442,0.332173,0.476797,0.430907,0.189406,0.350781,0.254351,0.460907,0.294795,0.394111,0.449167,0.457034,0.137392,0.00511241,0.205993,0.36471,0.199435,0.241617,0.288395,0.346951,0.490408,0.139281,0.283944,0.410253,0.366829,0.0963824,0.0919595,0.435422,0.105754,0.604018,0.572253,0.134512,0.226588,0.190466,0.0685693,0.238251,0.203945,0.203623,0.274311,0.666543,0.188879,0.1453,0.441018,0.565736,0.257797,0.416111,0.264998,0.655835,0.0141313,0.260762,0.0017376,0.197132,0.353785,0.263548,0.288625,0.183307,0.397115,0.270765,0.670799,0.514206,0.153367,0.0247803,0.180891,0.2135,0.40885,0.344773,0.559616,0.381495,0.662373,0.225154,0.68552,0.289967,0.430399,0.161511,0.609231,0.288897,0.371428,0.511854,0.560898,0.539159,0.509533,0.244574,0.234943,0.501916,0.807273,0.520027,0.276236,0.341467,0.236025,0.490999,0.507107,0.35852,0.518077,0.194436,0.606515,0.472484,0.309072,0.714953,0.770653,0.422571,0.315912,0.520537,0.40567,0.404233,0.591465,0.56501,0.350669,0.735189,0.710944,0.481208,0.365858,0.724934,0.377651,0.405448,0.106119,0.549109,0.337559,0.335334,0.188199,0.229683,0.307795,0.222465,0.521111,0.481364,0.0951588,0.231991,0.708055,0.209809,0.288813,0.315085,0.896324,0.245518,0.147225,0.0840433,0.456059,0.175141,0.129037,0.210204,0.593218,0.477305,0.395226,0.680415,0.662221,0.714573,0.594689,0.693124,0.0165771,0.614552,0.375122,0.578552,0.192023,0.61495,0.519066,0.653086,0.702572,0.196694,0.00169137,0.330741,0.186195,0.250419,0.220604,0.418223,0.397183,0.672514,0.390299,0.128953,0.62476,0.765768,0.586829,0.458812,0.0625141,0.434936,0.540325,0.135869,0.0172533,0.170508,0.155216,0.53004,0.515744,0.0104816,0.725503,0.701373,0.0673619,0.632793,0.0332172,0.0668819,0.5341,0.155633,0.294469,0.569916,0.0954693,0.601193,0.0763099,0.0661332,0.22502,0.24982,0.458667,0.626754,0.620775,0.631122,0.203476,0.723265,0.222378,0.285863,0.0202227,0.520724,0.0294803,0.200793,0.354709,0.22596,0.125088,0.182366,0.106908,0.42596,0.425001,0.693935,0.805213,0.0576032,0.175587,0.483093,0.0606947,0.663287,0.21039,0.502185,0.185362,0.834164,0.387521,0.626173,0.105878,0.70202,0.0536584,0.097178,0.413302,0.412658,0.135898,0.0149771,0.888582,0.261712,0.123966,0.476846,0.532861,0.546744,0.615272,0.314286,0.22929,0.0685732,0.565977,0.101483,0.330547,0.10694,0.897516,0.58615,0.423128,0.363368,0.581837,0.325248,0.0777222,0.402619,0.150559,0.117524,0.012429,0.165441,0.279498,0.794473,0.697504,0.597203,0.470865,0.464871,0.00026744,0.00612045,0.197337,0.714124,0.0615767,0.494844,0.088487,0.659707,0.198855,0.613492,0.601978,0.751403,0.369401,0.796325,0.278856,0.764115,0.292233,0.937663,0.647973,0.749242,0.320366,0.165069,0.351371,0.771738,0.574353,0.834501,0.61522,0.117041,0.356085,0.52315,0.40999,0.786665,1.39161e-05,0.262908,0.568687,0.296329,0.409794,0.262678,0.138097,0.231657,0.726945,0.0634914,0.276336,0.736443,0.53643,0.600958,0.537603,0.291253,0.635992,0.335704,0.352283,0.544901,0.716136,0.00131918,0.365581,0.635028,0.257162,0.575502,0.239404,0.294262,0.298493,0.110583,0.800547,0.655487,0.616898,0.591825,0.434669,0.618663,0.133755,0.345889,0.436693,0.576571,0.672083,0.413616,0.321311,0.456129,0.636701,0.34916,0.297189,0.260709,0.636901,0.388431,0.405516,0.494592,0.311707,0.042743,0.6759,0.19153,0.156425,0.256463,0.2073,0.182928,0.742383,0.62305,0.845837,0.517856,0.425875,0.362487,0.391951,0.233643,0.651499,0.526541,0.659873,0.242598,0.437148,0.728186,0.0781203,0.578172,0.529958,0.369264,0.507366,0.0917886,0.436325,0.0600595,0.588621,0.277718,0.726373,0.146359,0.0182303,0.647417,0.267219,0.484689,0.605197,0.711029,0.413837,0.301746,0.706001,0.199591,0.62065,0.479249,0.613776,0.696372,0.168881,0.456024,0.368578,0.664536,0.197903,0.569592,0.35714,0.624142,0.800209,0.418205,0.655776,0.310557,0.256206,0.38684,0.212386,0.0244906,0.508361,0.0491617,0.164865,0.212856,0.811886,0.378446,0.274825,0.593838,0.684324,0.0646415,0.307463,0.360772,0.249696,0.109994,0.24874,0.380462,0.257244,0.290861,0.449637,0.394043,0.177566,0.2594,0.334235,0.149754,0.4665,0.260863,0.196058,0.0612029,0.842292,0.484329,0.381419,0.722288,0.619978,0.673224,0.45399,0.718309,0.571568,0.177612,0.150017,0.457871,0.531832,0.264566,0.618193,0.430455,0.326182,0.818071,0.413389,0.288452,0.30024,0.411844,0.242131,0.60086,0.761628,0.422894,0.71245,0.541376,0.667256,0.34672,0.820943,0.670026,0.267686,0.353867,0.322489,0.808195,0.557903,0.173213,0.746229,0.273599,0.396837,0.0787568,0.664067,0.567651,0.523596,0.0902785,0.717141,0.631874,0.308071
}}
}}

Revision as of 12:46, 5 September 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
hematopoietic stem cell3.28e-46172
angioblastic mesenchymal cell3.28e-46172
leukocyte1.52e-44140
hematopoietic cell4.44e-43182
hematopoietic oligopotent progenitor cell6.38e-43165
hematopoietic multipotent progenitor cell6.38e-43165
hematopoietic lineage restricted progenitor cell8.16e-36124
nongranular leukocyte1.37e-34119
myeloid cell3.41e-27112
common myeloid progenitor3.41e-27112
myeloid leukocyte7.32e-2676
granulocyte monocyte progenitor cell3.52e-2271
CD14-positive, CD16-negative classical monocyte3.38e-2142
classical monocyte1.30e-2045
myeloid lineage restricted progenitor cell3.04e-2070
macrophage dendritic cell progenitor1.47e-1965
monopoietic cell1.53e-1863
monocyte1.53e-1863
monoblast1.53e-1863
promonocyte1.53e-1863
lymphoid lineage restricted progenitor cell5.34e-1452
lymphocyte6.07e-1453
common lymphoid progenitor6.07e-1453
mature alpha-beta T cell7.09e-1218
alpha-beta T cell7.09e-1218
immature T cell7.09e-1218
mature T cell7.09e-1218
immature alpha-beta T cell7.09e-1218
mesenchymal cell4.01e-11358
T cell4.29e-1125
pro-T cell4.29e-1125
connective tissue cell2.42e-10365
CD8-positive, alpha-beta T cell5.50e-0811
motile cell3.43e-07390
granulocyte8.46e-078
Uber Anatomy
Ontology termp-valuen
hematopoietic system1.84e-26102
blood island1.84e-26102
hemolymphoid system9.43e-24112
bone marrow6.92e-1880
bone element1.63e-1586
adult organism1.70e-14115
immune system1.74e-14115
skeletal element1.38e-11101
skeletal system1.38e-11101
connective tissue1.86e-08375
blood3.65e-0815
haemolymphatic fluid3.65e-0815
organism substance3.65e-0815


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.