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Coexpression cluster:C578: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002390!7.67e-14!102;UBERON:0003061!7.67e-14!102;UBERON:0002193!4.73e-13!112;UBERON:0002371!1.32e-10!80;UBERON:0001474!1.04e-09!86
|ontology_enrichment_uberon=UBERON:0002390!7.67e-14!102;UBERON:0003061!7.67e-14!102;UBERON:0002193!4.73e-13!112;UBERON:0002371!1.32e-10!80;UBERON:0001474!1.04e-09!86
|tf_chipseq_enrich=CTCF#10664;8:2.85880339897335:0.00268164727109909:0.0147723276199334!E2F1#1869;8:2.61727424793564:0.00478608560856321:0.0224906184419678!EBF1#1879;8:4.75011565150347:7.80369455890836e-05:0.00120225705271844!POLR2A#5430;12:1.71796254124646:0.00885747283887137:0.0336167456144664!TFAP2C#7022;5:3.60307620328674:0.00920612058381016:0.0348071544601437
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08,0.250037,0.672252,0.154781,0.882857,0.710461,0.182373,0.264717,0.75446,0.13973,0.438047,0.441658,0.44727,0.135062,0.109155,0.184301,0.179723,0.367181,0.24648,0.540592,0.768481,0.705816,0.651424,0.504688,0.0423521,0.155296,0.815718,0.326917,0.611971,0.34762,0.267461,0.604786,0.550255,0.00771961,0.599568,0.176102,0.372391,0.552552,0.504309,0.215174,0.392525,0.793051,0.509791,0.331688,0.439061,0.497452,0.505726,0.0716716,0.0324152,0.233675,0.407539,0.226368,0.273208,0.324685,0.388388,0.540612,0.158915,0.319809,0.222436,0.361114,0.777707,0.346331,0.509101,0.469911,0.289571,0.624641,0.210014,0.256564,0.216359,0.108278,0.269486,0.618557,0.0355198,0.30924,0.718381,0.513033,0.165697,0.488864,0.250422,0.238269,0.000493757,0.321495,0.707921,0.436169,0.294337,0.437654,0.223799,0.395767,0.683892,0.324936,0.208357,0.44227,0.305343,0.366795,0.565276,0.174777,0.509038,0.205654,0.24203,0.454777,0.386034,0.611817,0.425563,0.714314,0.254974,0.736792,0.326406,0.815556,0.562451,0.295181,0.127356,0.414762,0.588704,0.613121,0.875652,0.560447,0.276477,0.286981,0.192724,0.143959,0.57128,0.311354,0.382458,0.267022,0.541227,0.557937,0.400873,0.56927,0.606796,0.659114,0.521917,0.371329,0.765005,0.506462,0.469353,0.354726,0.866443,0.451391,0.44986,0.644026,0.617298,0.392405,0.784148,0.761188,0.531029,0.408774,0.438594,0.421442,0.451155,0.121414,0.066034,0.378227,0.81527,0.598846,0.648409,0.345883,0.640311,0.572397,0.557297,0.00391652,0.262554,0.171503,0.625604,0.707991,0.731202,0.267305,0.11688,0.167866,0.276393,0.504701,0.199217,0.511852,0.0573506,0.405124,0.949229,0.735674,0.731856,0.358433,0.329295,0.671595,0.30307,0.0114417,0.667134,0.718633,0.893837,0.0493716,0.429984,0.0742027,0.587266,0.773727,0.616781,0.0039988,0.650129,0.269192,0.560399,0.883816,0.169185,0.017753,0.724192,0.163551,0.525513,0.700761,0.812644,0.14418,0.373925,0.635452,0.818392,0.226351,0.0949671,0.816869,0.141133,0.630865,0.336704,0.212254,0.189525,0.343354,0.752041,0.759742,0.45091,0.494975,0.824822,0.585751,0.394582,0.414667,0.665289,0.550781,0.208543,0.778451,0.227309,0.242032,0.38206,0.0388378,0.679264,0.673328,0.68359,0.106624,0.436246,0.302573,0.363242,0.0366922,0.571999,0.533166,0.4952,0.396764,0.848562,0.374842,0.59123,0.730341,0.472945,0.812139,0.0255686,0.848553,0.632449,0.493733,0.485682,0.522032,0.737356,0.703164,0.308335,0.0209084,0.343123,0.848903,0.702119,0.169492,0.119401,0.739698,0.00928197,0.750356,0.749842,0.20287,0.790681,0.268459,0.317742,0.950773,0.526477,0.0589378,0.0650206,0.667852,0.352955,0.566905,0.233027,0.61828,0.32988,0.414141,0.314278,0.488706,0.195487,0.337176,0.237881,0.895277,0.0478251,0.314694,0.0783847,0.681926,0.17779,0.367114,0.800175,0.961958,0.838878,0.74833,0.901865,0.27774,0.272042,0.447043,0.101362,0.473482,0.764216,0.695171,0.366519,0.865486,0.71171,0.285398,0.666079,0.654574,0.817491,0.675104,0.840552,0.953968,0.811117,0.91854,0.620546,0.92196,0.79731,0.199654,0.799819,0.91173,0.835204,0.651586,0.61405,0.6678,0.193337,0.442655,0.60022,0.0149779,0.531956,0.564859,0.683257,0.621028,0.333365,0.802264,0.318846,0.15758,0.650589,0.776375,0.280017,0.311463,0.785326,0.588141,0.653553,0.589343,0.710222,0.32507,0.376218,0.394146,0.596813,0.76613,0.686514,0.771295,0.687453,0.568618,0.260073,0.659004,0.712952,0.71675,0.617892,0.844359,0.348031,0.669472,0.276715,0.482161,0.671228,0.15268,0.0871212,0.484299,0.62901,0.723773,0.485866,0.360598,0.156759,0.689106,0.758854,0.715585,0.294279,0.689303,0.458747,0.451227,0.544961,0.728315,0.0603376,0.373192,0.603116,0.178215,0.0466949,0.235131,0.207933,0.7909,0.675589,0.884374,0.569042,0.472855,0.405145,0.436753,0.264384,0.124063,0.577987,0.711872,0.66241,0.48478,0.443192,0.841236,0.630628,0.581499,0.437906,0.558205,0.12572,0.48391,0.638918,0.641165,0.31298,0.775835,0.780702,0.67999,0.699663,0.687511,0.534658,0.290834,0.419307,0.460081,0.719638,0.75647,0.613225,0.673203,0.528985,0.666362,0.747244,0.572915,0.504664,0.773508,0.716425,0.243842,0.621945,0.399385,0.676673,0.844055,0.229398,0.707863,0.00100453,0.676528,0.431288,0.240791,0.241466,0.559235,0.333781,0.187694,0.241313,0.854523,0.780673,0.694879,0.64641,0.735636,0.650372,0.345521,0.403299,0.282135,0.13864,0.281079,0.424456,0.29046,0.327384,0.497947,0.438989,0.201933,0.292836,0.0810722,0.170712,0.515655,0.681219,0.523107,0.815334,0.881301,0.534283,0.197939,0.434878,0.672536,0.724882,0.829964,0.768195,0.623948,0.811363,0.453963,0.506604,0.218634,0.321002,0.670761,0.503829,0.740494,0.860028,0.0246695,0.348129,0.718304,0.457962,0.661914,0.653454,0.808817,0.0880121,0.42125,0.593207,0.719076,0.388139,0.862574,0.721773,0.324561,0.0914016,0.361878,0.851225,0.610074,0.57891,0.794497,0.308457,0.793549,0.412853,0.715967,0.619978,0.574957,0.342733,0.767086,0.110499,0.893824
}}
}}

Revision as of 12:29, 5 September 2012


Full id: C578_CD34_Natural_CD8_CD4_CD133_Basophils_CD14



Phase1 CAGE Peaks

Hg19::chr10:12390958..12390973,-p@chr10:12390958..12390973
-
Hg19::chr12:76952682..76952690,-p@chr12:76952682..76952690
-
Hg19::chr13:101326316..101326335,+p@chr13:101326316..101326335
+
Hg19::chr14:105760706..105760717,-p@chr14:105760706..105760717
-
Hg19::chr14:105760904..105760918,+p@chr14:105760904..105760918
+
Hg19::chr15:52970999..52971015,+p@chr15:52970999..52971015
+
Hg19::chr15:52971052..52971073,+p@chr15:52971052..52971073
+
Hg19::chr19:33865006..33865017,-p@chr19:33865006..33865017
-
Hg19::chr1:221916028..221916038,+p@chr1:221916028..221916038
+
Hg19::chr2:122457110..122457118,-p@chr2:122457110..122457118
-
Hg19::chr2:28571261..28571277,+p@chr2:28571261..28571277
+
Hg19::chr6:16762361..16762374,-p@chr6:16762361..16762374
-
Hg19::chr6:34205792..34205795,-p@chr6:34205792..34205795
-
Hg19::chr7:141401439..141401452,+p@chr7:141401439..141401452
+
Hg19::chr8:145013517..145013546,+p@chr8:145013517..145013546
+


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
leukocyte6.23e-32140
hematopoietic stem cell9.33e-31172
angioblastic mesenchymal cell9.33e-31172
hematopoietic cell3.75e-29182
hematopoietic oligopotent progenitor cell3.26e-27165
hematopoietic multipotent progenitor cell3.26e-27165
hematopoietic lineage restricted progenitor cell3.23e-23124
nongranular leukocyte8.71e-22119
CD14-positive, CD16-negative classical monocyte1.41e-1742
classical monocyte1.44e-1545
myeloid cell4.10e-15112
common myeloid progenitor4.10e-15112
myeloid leukocyte1.17e-1476
lymphoid lineage restricted progenitor cell2.42e-1252
granulocyte monocyte progenitor cell2.42e-1271
lymphocyte7.16e-1253
common lymphoid progenitor7.16e-1253
myeloid lineage restricted progenitor cell1.77e-1070
mature alpha-beta T cell4.37e-1018
alpha-beta T cell4.37e-1018
immature T cell4.37e-1018
mature T cell4.37e-1018
immature alpha-beta T cell4.37e-1018
macrophage dendritic cell progenitor6.05e-1065
T cell3.17e-0925
pro-T cell3.17e-0925
monopoietic cell4.11e-0963
monocyte4.11e-0963
monoblast4.11e-0963
promonocyte4.11e-0963
Uber Anatomy
Ontology termp-valuen
hematopoietic system7.67e-14102
blood island7.67e-14102
hemolymphoid system4.73e-13112
bone marrow1.32e-1080
bone element1.04e-0986


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
CTCF#1066482.858803398973350.002681647271099090.0147723276199334
E2F1#186982.617274247935640.004786085608563210.0224906184419678
EBF1#187984.750115651503477.80369455890836e-050.00120225705271844
POLR2A#5430121.717962541246460.008857472838871370.0336167456144664
TFAP2C#702253.603076203286740.009206120583810160.0348071544601437



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.