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Coexpression cluster:C1175: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002390!1.57e-16!102;UBERON:0003061!1.57e-16!102;UBERON:0002193!5.75e-15!112;UBERON:0007023!1.04e-12!115;UBERON:0002371!2.78e-09!80;UBERON:0001474!9.20e-08!86;UBERON:0000178!1.80e-07!15;UBERON:0000179!1.80e-07!15;UBERON:0000463!1.80e-07!15
|ontology_enrichment_uberon=UBERON:0002390!1.57e-16!102;UBERON:0003061!1.57e-16!102;UBERON:0002193!5.75e-15!112;UBERON:0007023!1.04e-12!115;UBERON:0002371!2.78e-09!80;UBERON:0001474!9.20e-08!86;UBERON:0000178!1.80e-07!15;UBERON:0000179!1.80e-07!15;UBERON:0000463!1.80e-07!15
|tf_chipseq_enrich=NFKB1#4790;6:4.70405436359472:0.00021611506140197:0.00247704575260759!SUZ12#23512;2:14.318794546018:0.00781968192361486:0.0321186046494047
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46629,0.00254966,0.00300323,0.177111,0.167984,0.337564,0.394053,0.00795414,0.17256,0.126216,0.0947479,0.0787488,0.0883646,0.496336,0.353144,0.407665,0.11039,0.361507,0.660283,0.0754745,0.632378,0.439214,0.0896836,0.133679,0.718626,0.262768,0.235824,0.0309143,0.506939,0.0654706,0.554729,0.305348,0.0883079,0.192275,0.123717,0.3044,0.00527825,0.435034,0.0137751,0.27954,0.689314,0.468189,0.187355,0.168686,0.35711,0.180717,0.375467,0.614081,4.41005e-05,0.299453,0.000987635,0.000491774,0.195385,0.578705,0.546003,0.106912,0.207535,0.747423,0.283013,0.17144,0.236468,0.274647,0.280244,0.753667,0.164035,0.1168,0.0253961,0.112879,0.138362,0.0148661,0.0226215,0.304414,0.0775871,0.1646,0.00753056,0.956744,0.709639,0.000316835,0.190081,0.25636,0.392755,0.366993,0.843094,0.12921,0.107541,0.688004,0.136306,0.362226,0.0104549,0.158567,0.446426,0.192217,0.00337841,0.268889,0.361819,0.97666,0.98796,0.417001,0.113527,0.234633,0.150144,0.235575,0.111506,0.209512,0.415762,0.0148926,0.1033,0.238509,0.156356,0.0229455,0.322099,0.0857464,0.282499,0.101873,0.121306,0.246526,0.203595,0.0730406,0.0282156,0.44271,0.128341,0.463619,0.168391,0.545636,0.320047,0.397073,0.437057,0.221207,0.603174,0.358,0.621995,0.318595,0.140173,0.390753,0.312917,0.805801,0.0602813,0.15977,0.201434,0.134947,0.304849,0.316782,0.212636,0.325012,0.0010615,0.0908811,0.291345,0.453507,0.491263,0.00881004,0.035987,0.184894,0.609179,0.244347,0.00293678,0.00153446,0.361244,0.207462,0.00620403,0.0303991,0.29768,0.217499,0.154075,0.00229459,0.0325908,0.0586175,0.0694648,0.198885,0.871901,0.347052,0.386025,0.1797,0.379465,0.327304,0.581915,0.498434,0.132491,0.48467,0.367752,0.436987,0.0244296,0.704893,0.392559,0.0821811,0.129258,0.279549,0.0984834,0.284421,0.71736,0.658832,0.751141,0.00163422,0.458949,0.547863,0.0124088,0.29302,0.726427,0.0525879,0.401507,0.330231,0.648881,0.703424,0.673541,0.86822,0.910041,0.380231,0.799099,0.110853,0.790371,0.802111,0.744931,0.249855,0.954926,0.991631,0.122261,0.818359,0.894024,0.315577,0.0448062,0.487781,0.558605,0.952537,0.54891,0.341975,0.765292,0.547149,0.592518,0.448065,0.0724603,0.771117,0.154752,0.74852,0.478352,0.864643,0.685599,0.814936,0.931591,0.0645985,0.834663,0.434172,0.797881,0.976385,0.664234,0.873084,0.19467,0.692633,0.829635,0.96824,0.411785,0.40673,0.415502,0.565657,0.499305,0.726141,0.632958,0.676266,0.327011,0.299176,0.710278,0.210121,0.585578,0.640275,0.341296,0.457524,1.55061e-05,0.184142,0.574271,0.585566,0.0120148,0.538803,0.867555,0.0266435,0.346345,0.00184886,0.596462,0.917146,0.252282,0.645172,0.681127,0.821879,0.727983,0.536712,0.443364,0.715629,0.715255,0.425138,0.814568,0.599651,0.41419,0.0543219,0.294507,0.734868,8.22035e-05,0.40211,0.183851,0.0608535,0.45175,0.362009,0.611179,0.0251037,0.0315798,0.126341,0.654039,0.832266,0.0301369,0.283731,0.466416,0.411899,0.525367,0.300829,0.0515585,0.635414,0.528332,0.0918183,0.0551791,0.0276663,0.661532,0.574524,0.570287,0.797742,0.68023,0.808962,0.00505324,0.105241,0.760368,0.00676553,0.440345,0.232264,0.400622,0.391073,0.766374,0.363579,0.0559361,0.420733,0.540565,0.30566,0.775603,0.695855,0.0398223,0.000844968,0.173588,0.312949,0.195343,0.278413,0.620377,0.402066,0.887664,0.00634025,0.610982,0.523153,0.0103557,0.679978,0.101471,0.364157,0.172412,0.53064,0.101365,0.0769041,0.0873978,0.155446,0.0861933,0.159832,0.512288,0.338978,0.390233,0.339879,0.0210008,0.41967,0.197678,0.208523,0.34551,0.148216,0.026431,0.497662,0.103429,0.0135943,0.369586,0.394729,0.441472,0.444932,0.622992,0.215866,0.436618,0.403472,0.382758,0.264429,0.0960556,0.0744027,0.204325,0.265849,0.370442,0.451398,0.0421649,0.0189729,0.279598,0.420279,0.485091,0.443868,0.150111,0.420451,0.00644063,0.0326037,0.0530412,0.455626,0.0650142,0.454846,0.350305,0.0875262,0.147486,0.117583,0.103076,0.518238,0.40865,0.266737,0.0596356,0.25829,0.215261,0.235004,0.00933588,0.111352,0.331422,0.440492,0.397558,0.266168,0.156298,0.0115214,0.0797171,0.334024,0.153743,0.316975,0.435107,0.26559,0.0828289,0.0836911,0.160696,0.155054,0.15862,0.0999718,0.0194676,2.23638e-05,0.300222,0.393729,0.487504,0.249956,0.447581,0.482721,0.35808,0.016105,0.296254,0.400859,0.473667,0.327684,0.279523,0.499937,0.444635,0.356463,0.364875,0.211724,0.0165104,0.215534,0.536787,0.436872,0.181464,0.40945,0.231548,0.120636,0.121001,0.317719,0.172653,0.0924531,0.120918,0.227375,0.507382,0.425328,0.384398,0.00378776,0.00163336,0.179489,0.214126,0.143317,0.00371239,0.14273,0.227254,0.147968,0.168955,0.274981,0.236422,0.00516624,0.149301,0.196723,0.0836477,0.00501836,0.413461,0.050072,0.187007,0.630108,0.299959,0.160183,0.498355,0.406059,0.452427,0.200877,0.149642,0.366448,0.183454,0.161573,0.043754,0.0638873,0.102233,0.404559,0.00866241,0.131715,0.0143467,0.249647,0.43669,0.119023,0.248584,0.0148527,0.390152,0.0012091,0.540199,0.488863,0.342785,0.119442,0.20487,0.0147917,0.0228215,0.41929,0.209566,0.189123,0.0610821,0.355645,0.332105,0.0389799,0.158122,0.00684504,0.00212496,0.444217,0.363335,0.00788691,0.00274698,0.00520345,0.00228043,0.000750837
}}
}}

Revision as of 12:19, 5 September 2012


Full id: C1175_Mast_CD14_Natural_CD19_Eosinophils_Basophils_CD8



Phase1 CAGE Peaks

Hg19::chr12:76479393..76479404,-p@chr12:76479393..76479404
-
Hg19::chr19:10714716..10714736,-p@chr19:10714716..10714736
-
Hg19::chr3:42055874..42055894,-p@chr3:42055874..42055894
-
Hg19::chr6:157101752..157101763,+p@chr6:157101752..157101763
+
Hg19::chr8:61822237..61822249,+p3@ENST00000526936
Hg19::chr8:61822258..61822293,+p1@ENST00000526936
Hg19::chr8:61822305..61822316,+p5@ENST00000526936


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
leukocyte2.97e-45140
hematopoietic stem cell1.97e-36172
angioblastic mesenchymal cell1.97e-36172
hematopoietic cell3.21e-35182
hematopoietic lineage restricted progenitor cell1.31e-34124
nongranular leukocyte2.78e-34119
hematopoietic oligopotent progenitor cell8.41e-32165
hematopoietic multipotent progenitor cell8.41e-32165
lymphocyte5.51e-2753
common lymphoid progenitor5.51e-2753
lymphoid lineage restricted progenitor cell1.88e-2652
lymphocyte of B lineage8.54e-1624
pro-B cell8.54e-1624
CD14-positive, CD16-negative classical monocyte3.55e-1542
myeloid leukocyte5.82e-1476
classical monocyte2.24e-1345
B cell1.01e-1114
mature alpha-beta T cell2.28e-1118
alpha-beta T cell2.28e-1118
immature T cell2.28e-1118
mature T cell2.28e-1118
immature alpha-beta T cell2.28e-1118
granulocyte monocyte progenitor cell1.43e-1071
myeloid lineage restricted progenitor cell4.01e-1070
myeloid cell6.83e-10112
common myeloid progenitor6.83e-10112
T cell1.63e-0925
pro-T cell1.63e-0925
intermediate monocyte2.17e-099
CD14-positive, CD16-positive monocyte2.17e-099
macrophage dendritic cell progenitor3.23e-0965
monopoietic cell1.80e-0863
monocyte1.80e-0863
monoblast1.80e-0863
promonocyte1.80e-0863
mesenchymal cell1.03e-07358
connective tissue cell5.44e-07365
Uber Anatomy
Ontology termp-valuen
hematopoietic system1.57e-16102
blood island1.57e-16102
hemolymphoid system5.75e-15112
adult organism1.04e-12115
bone marrow2.78e-0980
bone element9.20e-0886
blood1.80e-0715
haemolymphatic fluid1.80e-0715
organism substance1.80e-0715


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
NFKB1#479064.704054363594720.000216115061401970.00247704575260759
SUZ12#23512214.3187945460180.007819681923614860.0321186046494047



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.