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Coexpression cluster:C1488: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002193!6.64e-29!112;UBERON:0002390!1.97e-28!102;UBERON:0003061!1.97e-28!102;UBERON:0002371!3.81e-22!80;UBERON:0001474!4.78e-18!86;UBERON:0002405!1.25e-17!115;UBERON:0004765!1.05e-12!101;UBERON:0001434!1.05e-12!101;UBERON:0003081!4.78e-09!216;UBERON:0007023!6.75e-08!115
|ontology_enrichment_uberon=UBERON:0002193!6.64e-29!112;UBERON:0002390!1.97e-28!102;UBERON:0003061!1.97e-28!102;UBERON:0002371!3.81e-22!80;UBERON:0001474!4.78e-18!86;UBERON:0002405!1.25e-17!115;UBERON:0004765!1.05e-12!101;UBERON:0001434!1.05e-12!101;UBERON:0003081!4.78e-09!216;UBERON:0007023!6.75e-08!115
|tf_chipseq_enrich=ELF1#1997;6:4.25809795880754:0.000167722477628883:0.00205330768269639!POLR2A#5430;6:2.14745317655807:0.0101957067681878:0.0380513657505277!SRF#6722;3:6.8985891310839:0.0064424516893037:0.0280036297489986!TAF1#6872;6:3.34304628574529:0.000716247428463562:0.00573475660696918
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81783,0.0678906,0.076236,0.444489,0.31161,0.361651,0.0953991,0.319245,0.0671053,0.0650516,0.575882,0.390908,0.0773818,0.115736,0.662745,0.229952,0.205891,0.207936,0.123916,0.0563868,0.0780087,0.268235,0.0761868,0.167255,0.107028,0.267379,0.443026,0.387018,0.343977,0.244992,0.632847,0.417985,0.491614,0.146453,0.315229,0.157053,0.332022,0.19701,0.273582,0.262915,0.306556,0.26147,0.170005,0.523331,0.491788,0.092369,0.18076,0.11609,0.248113,0.148878,0.206465,0.240599,0.245625,0.0313577,0.3342,0.100989,0.188919,0.0975693,0.119835,0.145322,0.178533,0.267392,0.0668831,0.142859,0.477403,0.135899,0.881177,0.387334,0.149927,0.224219,0.347904,0.324262,0.0771032,0.111827,0.0929171,0.63152,0.118035,0.319902,0.510835,0.137556,0.397628,0.49748,0.0699003,0.235435,0.31953,0.0584492,0.00449343,0.0790496,0.388777,0.204831,0.130161,0.205669,0.0963721,0.182511,0.369139,0.145449,0.0892237,0.208284,0.00964187,0.401189,0.283386,0.0739625,0.247651,0.0879809,0.104922,0.215434,0.177269,0.31512,0.198881,0.394164,0.111068,0.4137,0.146194,0.0313058,0.281527,0.0708038,0.3889,0.192889,0.0463105,0.316041,0.565635,0.280212,0.121421,0.346061,0.275075,0.0144415,0.287361,0.138613,0.175356,0.116846,0.267784,0.278571,0.185281,0.286026,0.054558,0.349805,0.255609,0.404239,0.439697,0.493192,0.223892,0.0136721,0.553042,0.213489,0.212611,0.338443,0.319005,0.180695,0.45842,0.436073,0.261316,0.189596,0.448839,0.196587,0.213353,0.0504588,0.307626,0.173101,0.259063,0.306056,0.341713,0.156156,0.0639829,0.0461852,0.0401725,0.419951,0.114697,0.111558,0.324956,0.388835,0.408751,0.000748996,0.131285,0.070868,0.0921869,0.245,0.0850317,0.249379,0.294768,0.60218,0.11882,0.281293,0.409327,0.792771,0.685907,0.603176,0.670776,0.696176,0.355968,0.636386,0.592254,0.647186,0.616927,0.82397,0.15467,0.677416,0.725074,0.628346,0.387005,0.163758,0.689958,0.772379,0.599685,0.230665,0.402631,0.429394,0.302735,0.255824,0.488239,0.410034,0.0795949,0.48468,0.494578,0.301433,0.711296,0.492887,0.245317,0.727698,0.559471,0.717449,0.449761,0.6937,0.427531,0.353735,0.629087,0.275995,0.200465,0.297082,0.526245,0.342233,0.746016,0.221303,0.240506,0.197504,0.37236,0.366986,0.296598,0.177522,0.36546,0.360788,0.368898,0.510705,0.447298,0.670481,0.576455,0.619669,0.287839,0.262665,0.654187,0.183051,0.530004,0.583703,0.300816,0.407994,0.225997,0.487688,0.491994,0.529993,0.329919,0.484887,0.583109,0.57085,0.650025,0.179563,0.540605,0.881739,0.563634,0.122712,0.624569,0.435062,0.0471347,0.785953,0.394773,0.659669,0.292434,0.711322,0.0530046,0.516717,0.367684,0.700165,0.258457,0.188291,0.305952,0.356524,0.159817,0.532764,0.730276,0.319704,0.555004,0.240491,0.773067,0.650555,0.597394,0.783534,0.261107,0.594475,0.416321,0.365565,0.0271165,0.610358,0.693748,0.578885,0.474879,0.0176389,0.518205,0.424119,0.60488,0.519279,0.16418,0.39773,0.623664,0.757999,0.438945,0.0742738,0.706112,0.754688,0.39196,0.416041,0.355152,0.346355,0.712437,0.0395208,0.520214,0.708106,0.486574,0.0870562,0.366382,0.639482,0.471879,0.600697,0.474504,0.621275,0.727464,0.589415,0.564042,0.356483,0.28925,0.624316,0.55481,0.191884,0.509842,0.597297,0.368631,0.321667,0.149733,0.477082,0.368449,0.066291,0.343349,0.450702,0.341084,0.138667,0.459605,0.298707,0.345583,0.299527,0.390707,0.372757,0.172033,0.181635,0.304651,0.440771,0.613566,0.445744,0.371991,0.694395,0.326635,0.349721,0.39301,0.396235,0.566617,0.524829,0.388491,0.357781,0.338712,0.231439,0.359148,0.0641227,0.177916,0.232711,0.327419,0.402268,0.479755,0.163801,0.245045,0.080461,0.433875,0.395243,0.130132,0.373481,0.462042,0.213394,0.270174,0.406219,0.298,0.40549,0.30902,0.0755079,0.12783,0.101672,0.0890286,0.465261,0.362561,0.578088,0.285875,0.225945,0.18761,0.20516,0.115576,0.385234,0.291842,0.392097,0.352327,0.232997,0.451856,0.521039,0.328594,0.294205,0.448388,0.278746,0.387086,0.232479,0.334662,0.336321,0.139427,0.450171,0.454978,0.366035,0.381922,0.372037,0.263608,0.3488,0.43615,0.218495,0.398705,0.431643,0.316114,0.360691,0.26003,0.35537,0.423126,0.288449,0.244977,0.447896,0.395958,0.314638,0.322324,0.184473,0.363414,0.524458,0.482957,0.0138042,0.157712,0.3633,0.202084,0.104337,0.104656,0.279419,0.149946,0.0797883,0.104584,0.537494,0.454949,0.378002,0.340219,0.412672,0.343186,0.155969,0.186603,0.124175,0.228962,0.12366,0.198264,0.128253,0.14669,0.240899,0.206424,0.0862744,0.129421,0.171188,0.0721407,0.251724,0.36701,0.504058,0.491191,0.573638,0.263371,0.457065,0.446399,0.360168,0.403229,0.507716,0.442751,0.323763,0.486842,0.458912,0.246162,0.295506,0.369944,0.0738345,0.491474,0.417013,0.544575,0.21822,0.388558,0.397562,0.21727,0.351946,0.345508,0.484083,0.486223,0.437432,0.302171,0.398223,0.178399,0.547908,0.400541,0.372405,0.182559,0.164471,0.533328,0.313891,0.292462,0.46896,0.137165,0.467981,0.191837,0.395568,0.320916,0.289812,0.384881,0.441686,0.369492,0.592234
}}
}}

Revision as of 13:39, 5 September 2012


Full id: C1488_CD4_CD19_CD14CD16_CD8_Neutrophils_Basophils_Natural



Phase1 CAGE Peaks

Hg19::chr21:43482969..43482994,+p2@UMODL1
Hg19::chr4:83295323..83295348,+p@chr4:83295323..83295348
+
Hg19::chr5:1386528..1386539,-p2@AK127466
Hg19::chr7:144533055..144533069,-p2@TPK1
Hg19::chr8:132916684..132916697,-p@chr8:132916684..132916697
-
Hg19::chr9:115095363..115095398,+p@chr9:115095363..115095398
+


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:0042357thiamin diphosphate metabolic process0.00144820886924134
GO:0004788thiamin diphosphokinase activity0.00144820886924134
GO:0009229thiamin diphosphate biosynthetic process0.00144820886924134
GO:0042724thiamin and derivative biosynthetic process0.00144820886924134
GO:0006772thiamin metabolic process0.00144820886924134
GO:0042723thiamin and derivative metabolic process0.00201134199617551
GO:0016778diphosphotransferase activity0.00482658131089662
GO:0006767water-soluble vitamin metabolic process0.0192921145785954
GO:0006766vitamin metabolic process0.0230358905860548
GO:0009108coenzyme biosynthetic process0.0469337764260271
GO:0051188cofactor biosynthetic process0.0481194432595581



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
leukocyte1.39e-52140
hematopoietic stem cell5.32e-48172
angioblastic mesenchymal cell5.32e-48172
hematopoietic cell1.46e-44182
hematopoietic oligopotent progenitor cell5.36e-44165
hematopoietic multipotent progenitor cell5.36e-44165
nongranular leukocyte1.43e-42119
hematopoietic lineage restricted progenitor cell1.79e-42124
myeloid leukocyte1.31e-2576
myeloid cell1.17e-22112
common myeloid progenitor1.17e-22112
granulocyte monocyte progenitor cell2.22e-2271
CD14-positive, CD16-negative classical monocyte8.90e-2142
macrophage dendritic cell progenitor1.22e-2065
myeloid lineage restricted progenitor cell1.53e-2070
lymphoid lineage restricted progenitor cell2.69e-2052
lymphocyte3.36e-2053
common lymphoid progenitor3.36e-2053
monopoietic cell7.03e-2063
monocyte7.03e-2063
monoblast7.03e-2063
promonocyte7.03e-2063
classical monocyte1.05e-1945
mature alpha-beta T cell1.95e-1118
alpha-beta T cell1.95e-1118
immature T cell1.95e-1118
mature T cell1.95e-1118
immature alpha-beta T cell1.95e-1118
T cell6.67e-1125
pro-T cell6.67e-1125
lymphocyte of B lineage6.08e-0924
pro-B cell6.08e-0924
CD8-positive, alpha-beta T cell4.20e-0811
B cell1.04e-0714
intermediate monocyte7.79e-079
CD14-positive, CD16-positive monocyte7.79e-079
mesenchymal cell8.12e-07358
Uber Anatomy
Ontology termp-valuen
hemolymphoid system6.64e-29112
hematopoietic system1.97e-28102
blood island1.97e-28102
bone marrow3.81e-2280
bone element4.78e-1886
immune system1.25e-17115
skeletal element1.05e-12101
skeletal system1.05e-12101
lateral plate mesoderm4.78e-09216
adult organism6.75e-08115


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#199764.258097958807540.0001677224776288830.00205330768269639
POLR2A#543062.147453176558070.01019570676818780.0380513657505277
SRF#672236.89858913108390.00644245168930370.0280036297489986
TAF1#687263.343046285745290.0007162474284635620.00573475660696918



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.