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Difference between revisions of "Coexpression cluster:C1312"

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|tf_chipseq_enrich=ELF1#1997;5:3.54841496567295:0.00344683777572169:0.0175225998081483!ELK4#2005;3:8.11784082923401:0.00405611313418576:0.0194061294434572!GABPB1#2553;4:4.71178922412145:0.00473005431155596:0.0222844705090488!IRF1#3659;4:5.09144250237593:0.00353524076589381:0.0179423175405376!MAX#4149;4:4.30170367267141:0.00664492391067637:0.0282914475461528!NANOG#79923;3:14.6223892405063:0.00073945629288338:0.00582501702914824!NFE2#4778;2:25.734753550543:0.00242996970902926:0.0136884361618828!PAX5#5079;4:4.44637702078522:0.00587473351924079:0.0263564282836887!POLR2A#5430;6:2.14745317655807:0.0101957067681878:0.0379834992923866!RFX5#5993;4:8.0319405514634:0.000620461542838141:0.00510923149668632!SIN3A#25942;5:4.50740393901261:0.00109611006120864:0.00765781247458484!SMARCB1#6598;3:9.12635789057871:0.00290024715036702:0.0156747522323112!SPI1#6688;5:6.83693625710227:0.000144964177397403:0.00188541889454638!TAF1#6872;5:2.78587190478774:0.0107863634029041:0.0397837620933711!TBP#6908;5:3.08897557258032:0.00664544827578693:0.0282786934146156!THAP1#55145;2:10.4563815342838:0.0139914785110365:0.0491161985887582!USF1#7391;4:4.24099951813864:0.00700536775082942:0.0295980259124104!ZNF143#7702;3:6.75043827611395:0.00685025920446858:0.0290331231659563!ZNF263#10127;4:5.48122775800712:0.00267560938060723:0.0147413994567017
 
|tf_chipseq_enrich=ELF1#1997;5:3.54841496567295:0.00344683777572169:0.0175225998081483!ELK4#2005;3:8.11784082923401:0.00405611313418576:0.0194061294434572!GABPB1#2553;4:4.71178922412145:0.00473005431155596:0.0222844705090488!IRF1#3659;4:5.09144250237593:0.00353524076589381:0.0179423175405376!MAX#4149;4:4.30170367267141:0.00664492391067637:0.0282914475461528!NANOG#79923;3:14.6223892405063:0.00073945629288338:0.00582501702914824!NFE2#4778;2:25.734753550543:0.00242996970902926:0.0136884361618828!PAX5#5079;4:4.44637702078522:0.00587473351924079:0.0263564282836887!POLR2A#5430;6:2.14745317655807:0.0101957067681878:0.0379834992923866!RFX5#5993;4:8.0319405514634:0.000620461542838141:0.00510923149668632!SIN3A#25942;5:4.50740393901261:0.00109611006120864:0.00765781247458484!SMARCB1#6598;3:9.12635789057871:0.00290024715036702:0.0156747522323112!SPI1#6688;5:6.83693625710227:0.000144964177397403:0.00188541889454638!TAF1#6872;5:2.78587190478774:0.0107863634029041:0.0397837620933711!TBP#6908;5:3.08897557258032:0.00664544827578693:0.0282786934146156!THAP1#55145;2:10.4563815342838:0.0139914785110365:0.0491161985887582!USF1#7391;4:4.24099951813864:0.00700536775082942:0.0295980259124104!ZNF143#7702;3:6.75043827611395:0.00685025920446858:0.0290331231659563!ZNF263#10127;4:5.48122775800712:0.00267560938060723:0.0147413994567017
 
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06,0.076236,0.444489,0.31161,0.361651,0.0953991,0.319245,0.0671053,0.0650516,0.575882,0.390908,0.0773818,0.115736,0.662745,0.229952,0.205891,0.207936,0.454529,0.0563868,0.473176,0.268235,0.0761868,0.167255,0.107028,0.267379,0.443026,0.387018,0.343977,0.244992,0.264969,0.417985,0.147684,0.146453,0.315229,0.157053,0.332022,0.19701,0.273582,0.262915,0.306556,0.26147,0.170005,0.523331,0.491788,0.092369,0.18076,0.692556,0.248113,0.148878,0.206465,0.240599,0.245625,0.674943,0.3342,0.100989,0.188919,0.0975693,0.119835,0.145322,0.178533,0.267392,0.0668831,0.142859,0.477403,0.135899,0.167086,0.387334,0.494914,0.224219,0.0690914,0.324262,0.471029,0.111827,0.0929171,0.63152,0.118035,0.319902,0.510835,0.137556,0.397628,0.49748,0.0699003,0.235435,0.31953,0.1177,0.643491,0.370285,0.388777,0.204831,0.130161,0.205669,0.0963721,0.182511,0.0785202,0.145449,0.0892237,0.208284,0.135613,0.401189,0.283386,0.0739625,0.247651,0.0879809,0.104922,0.215434,0.177269,0.31512,0.198881,0.394164,0.111068,0.4137,0.146194,0.491435,0.281527,0.35188,0.3889,0.192889,0.547162,0.316041,0.565635,0.280212,0.121421,0.346061,0.275075,0.409805,0.287361,0.138613,0.175356,0.116846,0.267784,0.278571,0.185281,0.286026,0.31159,0.349805,0.255609,0.404239,0.439697,0.148754,0.223892,0.160738,0.553042,0.213489,0.212611,0.338443,0.319005,0.180695,0.45842,0.436073,0.261316,0.189596,0.448839,0.196587,0.213353,0.0504588,0.307626,0.173101,0.828194,0.306056,0.341713,0.0128817,0.33569,0.288104,0.526446,0.174852,0.114697,0.433479,0.0596788,0.0879043,0.0980391,0.281184,0.305648,0.070868,0.28729,0.245,0.0850317,0.249379,0.02451,0.60218,0.696439,0.281293,0.409327,0.466607,0.685907,0.603176,0.670776,0.696176,0.355968,0.268531,0.592254,0.0881515,0.616927,0.82397,0.611131,0.312447,0.725074,0.628346,0.387005,0.750579,0.326884,0.186168,0.242552,0.230665,0.402631,0.429394,0.302735,0.623606,0.488239,0.754734,0.218104,0.48468,0.494578,0.301433,0.352623,0.492887,0.509735,0.727698,0.559471,0.717449,0.449761,0.6937,0.427531,0.353735,0.629087,0.130457,0.403716,0.297082,0.526245,0.342233,0.159416,0.622334,0.240506,0.369581,0.72684,0.195513,0.144373,0.177522,0.0768361,0.360788,0.368898,0.510705,0.447298,0.304675,0.576455,0.619669,0.287839,0.262665,0.654187,0.183051,0.530004,0.218878,0.300816,0.407994,0.225997,0.487688,0.808511,0.529993,0.0616477,0.484887,0.359097,0.57085,0.650025,0.0164693,0.540605,0.167995,0.563634,0.561918,0.624569,0.0630128,0.628517,0.455987,0.394773,0.659669,0.659285,0.352655,0.130129,0.516717,0.367684,0.700165,0.258457,0.188291,0.305952,0.0728342,0.159817,0.532764,0.730276,0.319704,0.555004,0.607569,0.773067,0.283145,0.597394,0.783534,0.628973,0.594475,0.416321,0.365565,0.47205,0.610358,0.331346,0.578885,0.474879,0.148175,0.518205,0.106317,0.0676419,0.519279,0.515179,0.745866,0.623664,0.171067,0.438945,0.619652,0.706112,0.754688,0.0894513,0.416041,0.355152,0.346355,0.712437,0.280648,0.520214,0.708106,0.486574,0.231819,0.722202,0.639482,0.471879,0.600697,0.474504,0.621275,0.373171,0.223923,0.564042,0.356483,0.5588,0.624316,0.55481,0.777518,0.509842,0.866311,0.368631,0.321667,0.149733,0.477082,0.368449,0.066291,0.343349,0.450702,0.341084,0.138667,0.127016,0.298707,0.345583,0.299527,0.390707,0.372757,0.172033,0.0175963,0.304651,0.440771,0.613566,0.445744,0.371991,0.332112,0.326635,0.349721,0.39301,0.396235,0.566617,0.171264,0.388491,0.357781,0.338712,0.231439,0.359148,0.0641227,0.177916,0.232711,0.0606512,0.402268,0.479755,0.163801,0.245045,0.373321,0.433875,0.395243,0.130132,0.373481,0.462042,0.213394,0.270174,0.406219,0.298,0.40549,0.30902,0.0755079,0.12783,0.101672,0.0890286,0.465261,0.362561,0.578088,0.285875,0.225945,0.18761,0.20516,0.115576,0.086142,0.291842,0.392097,0.352327,0.232997,0.122302,0.521039,0.328594,0.0482846,0.448388,0.278746,0.387086,0.232479,0.334662,0.336321,0.139427,0.450171,0.454978,0.077098,0.381922,0.372037,0.263608,0.3488,0.0205291,0.218495,0.0928446,0.431643,0.316114,0.360691,0.26003,0.0723267,0.423126,0.288449,0.244977,0.447896,0.395958,0.314638,0.322324,0.184473,0.363414,0.170988,0.482957,0.388728,0.157712,0.3633,0.202084,0.00564296,0.104656,0.279419,0.0118501,0.0797883,0.104584,0.537494,0.454949,0.378002,0.340219,0.0169449,0.343186,0.155969,0.186603,0.124175,0.228962,0.12366,0.198264,0.128253,0.14669,0.240899,0.206424,0.0862744,0.129421,0.171188,0.0721407,0.251724,0.36701,0.504058,0.147397,0.573638,0.263371,0.457065,0.446399,0.360168,0.403229,0.507716,0.442751,0.323763,0.486842,0.458912,0.246162,0.295506,0.369944,0.358783,0.491474,0.417013,0.544575,0.21822,0.0137836,0.397562,0.21727,0.0708324,0.345508,0.484083,0.486223,0.437432,0.302171,0.398223,0.178399,0.189006,0.400541,0.372405,0.182559,0.164471,0.533328,0.313891,0.0476793,0.132855,0.137165,0.467981,0.191837,0.395568,0.00724778,0.289812,0.384881,0.116282,0.369492,0.592234
 +
|tfbs_overrepresentation_for_novel_motifs=1.12961,0.333388,0.436508,0.58616,0.393082,0.584466,0.662701,0.269608,0.267027,0.555913,0.553339,0.707204,0.223349,0.650887,0.391663,0.415981,0.889639,0.336106,0.664996,0.127969,0.436569,1.03374,0.576478,0.387783,0.483957,1.73319,0.202389,0.574247,0.396295,0.186644,0.530785,0.92701,0.302275,0.640661,1.67655,0.134746,0.35388,0.585658,1.5795,0.69481,0.355745,0.513952,0.323162,1.01199,0.636689,1.18176,0.66382,1.33909,0.304272,1.02586,0.745008,0.675919,0.149032,1.00488,1.15929,0.653901,0.400834,0.62023,0.547548,0.619193,0.968558,0.666252,0.737866,0.861462,0.684675,0.826413,1.24834,1.61834,0.916468,1.45553,0.500342,0.275507,0.146905,1.15727,0.218784,0.594475,0.192925,0.84426,0.913168,0.477584,0.240887,2.00082,0.684313,0.272514,1.10535,0.181326,0.126687,0.536262,0.771626,1.71797,1.34233,1.07807,0.94406,0.30974,0.393853,0.864356,1.23175,0.987239,0.776336,0.166235,0.330999,0.938327,0.981588,0.893363,0.814675,0.548668,0.877269,0.647343,0.483695,0.376529,0.44815,0.978783,0.430775,0.563054,1.29401,0.352243,0.460936,0.529546,0.824029,0.312699,1.14892,0.769145,0.581628,0.695878,1.40534,0.845034,0.656181,0.949126,1.1919,0.324369,2.44613,0.53374,1.20639,0.692462,1.35529,0.520084,1.30187,0.57483,1.31259,2.17352,1.7705,1.27501,0.657956,0.983666,0.816466,0.611524,0.799467,2.01411,0.510514,0.306342,0.8388,0.0926553,1.07915,0.258882,0.665754,1.48627,0.755083,0.378604,0.484017,0.454152,1.27379,1.06043,0.912368,1.1583,0.83286,0.683502,0.79772,0.661335,0.152397
 
}}
 
}}

Revision as of 05:49, 26 November 2012


Full id: C1312_Eosinophils_Basophils_CD4_Natural_Mast_granulocyte_CD14CD16



Phase1 CAGE Peaks

Hg19::chr10:43932190..43932234,-p@chr10:43932190..43932234
-
Hg19::chr12:111028863..111028911,+p@chr12:111028863..111028911
+
Hg19::chr15:66084828..66084847,+p@chr15:66084828..66084847
+
Hg19::chr1:150980668..150980692,-p11@FAM63A
Hg19::chr2:86669343..86669357,-p@chr2:86669343..86669357
-
Hg19::chr3:53926081..53926105,+p@chr3:53926081..53926105
+


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
leukocyte6.29e-57136
hematopoietic stem cell1.68e-48168
angioblastic mesenchymal cell1.68e-48168
hematopoietic cell2.51e-45177
hematopoietic oligopotent progenitor cell5.39e-45161
hematopoietic multipotent progenitor cell5.39e-45161
nongranular leukocyte5.41e-45115
hematopoietic lineage restricted progenitor cell2.06e-43120
classical monocyte3.16e-3142
CD14-positive, CD16-negative classical monocyte3.16e-3142
myeloid leukocyte5.29e-2972
defensive cell6.36e-2548
phagocyte6.36e-2548
granulocyte monocyte progenitor cell2.30e-2467
myeloid cell2.86e-23108
common myeloid progenitor2.86e-23108
macrophage dendritic cell progenitor8.71e-2361
monopoietic cell1.19e-2159
monocyte1.19e-2159
monoblast1.19e-2159
promonocyte1.19e-2159
myeloid lineage restricted progenitor cell2.45e-2166
lymphocyte1.82e-2053
common lymphoid progenitor1.82e-2053
lymphoid lineage restricted progenitor cell5.45e-2052
nucleate cell4.42e-1955
mesenchymal cell1.22e-14354
connective tissue cell1.52e-14361
motile cell3.30e-13386
mature alpha-beta T cell6.81e-1218
alpha-beta T cell6.81e-1218
immature T cell6.81e-1218
mature T cell6.81e-1218
immature alpha-beta T cell6.81e-1218
B cell9.59e-1014
lymphocyte of B lineage1.21e-0924
pro-B cell1.21e-0924
T cell2.92e-0925
pro-T cell2.92e-0925
stuff accumulating cell8.39e-0987
intermediate monocyte1.55e-089
CD14-positive, CD16-positive monocyte1.55e-089
granulocyte1.73e-088
CD4-positive, alpha-beta T cell5.94e-076
CD8-positive, alpha-beta T cell9.60e-0711
Uber Anatomy
Ontology termp-valuen
hematopoietic system1.54e-2998
blood island1.54e-2998
hemolymphoid system7.58e-25108
bone marrow4.96e-2276
bone element1.84e-2082
immune system1.14e-1993
skeletal element5.43e-1890
skeletal system4.51e-14100
connective tissue1.09e-13371


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
ELF1#199753.548414965672950.003446837775721690.0175225998081483
ELK4#200538.117840829234010.004056113134185760.0194061294434572
GABPB1#255344.711789224121450.004730054311555960.0222844705090488
IRF1#365945.091442502375930.003535240765893810.0179423175405376
MAX#414944.301703672671410.006644923910676370.0282914475461528
NANOG#79923314.62238924050630.000739456292883380.00582501702914824
NFE2#4778225.7347535505430.002429969709029260.0136884361618828
PAX5#507944.446377020785220.005874733519240790.0263564282836887
POLR2A#543062.147453176558070.01019570676818780.0379834992923866
RFX5#599348.03194055146340.0006204615428381410.00510923149668632
SIN3A#2594254.507403939012610.001096110061208640.00765781247458484
SMARCB1#659839.126357890578710.002900247150367020.0156747522323112
SPI1#668856.836936257102270.0001449641773974030.00188541889454638
TAF1#687252.785871904787740.01078636340290410.0397837620933711
TBP#690853.088975572580320.006645448275786930.0282786934146156
THAP1#55145210.45638153428380.01399147851103650.0491161985887582
USF1#739144.240999518138640.007005367750829420.0295980259124104
ZNF143#770236.750438276113950.006850259204468580.0290331231659563
ZNF263#1012745.481227758007120.002675609380607230.0147413994567017



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.