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Coexpression cluster:C3218: Difference between revisions

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|full_id=C3218_CD14_Neutrophils_Eosinophils_Peripheral_Monocytederived_CD19_parietal
|full_id=C3218_CD14_Neutrophils_Eosinophils_Peripheral_Monocytederived_CD19_parietal
|id=C3218
|id=C3218
|ontology_enrichment_celltype=CL:0000766!1.48e-37!76;CL:0000738!1.26e-34!140;CL:0000557!1.95e-33!71;CL:0002009!1.03e-31!65;CL:0000839!2.26e-31!70;CL:0002194!7.26e-31!63;CL:0000576!7.26e-31!63;CL:0000040!7.26e-31!63;CL:0000559!7.26e-31!63;CL:0002031!1.90e-29!124;CL:0002087!2.88e-29!119;CL:0000860!2.65e-28!45;CL:0002057!1.88e-27!42;CL:0000037!4.71e-27!172;CL:0000566!4.71e-27!172;CL:0002032!9.04e-27!165;CL:0000837!9.04e-27!165;CL:0000763!1.38e-25!112;CL:0000049!1.38e-25!112;CL:0000988!1.02e-24!182
|ontology_enrichment_celltype=CL:0000766!3.36e-49!72;CL:0000557!1.21e-43!67;CL:0002009!2.79e-43!61;CL:0002194!3.99e-42!59;CL:0000576!3.99e-42!59;CL:0000040!3.99e-42!59;CL:0000559!3.99e-42!59;CL:0000473!1.37e-41!48;CL:0000234!1.37e-41!48;CL:0000839!1.95e-41!66;CL:0000860!1.47e-39!42;CL:0002057!1.47e-39!42;CL:0000738!1.90e-35!136;CL:0002031!5.24e-30!120;CL:0002087!6.63e-30!115;CL:0000763!5.04e-29!108;CL:0000049!5.04e-29!108;CL:0000037!2.43e-24!168;CL:0000566!2.43e-24!168;CL:0002032!7.72e-24!161;CL:0000837!7.72e-24!161;CL:0000988!2.06e-23!177;CL:0000325!1.10e-17!87;CL:0002393!5.22e-09!9;CL:0002397!5.22e-09!9
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002390!1.57e-32!102;UBERON:0003061!1.57e-32!102;UBERON:0001474!4.47e-29!86;UBERON:0002371!6.18e-29!80;UBERON:0002193!4.40e-27!112;UBERON:0004765!6.80e-25!101;UBERON:0001434!6.80e-25!101;UBERON:0002405!1.11e-14!115;UBERON:0002204!2.06e-09!167
|ontology_enrichment_uberon=UBERON:0002390!1.97e-39!98;UBERON:0003061!1.97e-39!98;UBERON:0002371!8.06e-38!76;UBERON:0001474!6.70e-36!82;UBERON:0002193!7.53e-35!108;UBERON:0004765!2.44e-30!90;UBERON:0002405!4.21e-30!93;UBERON:0001434!6.04e-29!100;UBERON:0002204!1.48e-11!167;UBERON:0003081!3.69e-10!203
|tf_chipseq_enrich=FAM48A#55578;1:385.05625:0.00259478966140747:0.0143491071400897
|tf_chipseq_enrich=FAM48A#55578;1:385.05625:0.00259478966140747:0.0143491071400897
|tfbs_overrepresentation=0.147255,0.0586687,0.35968,0.0477154,0.0214323,0.0460856,0.0430074,0.414564,0.03272,0.0257057,0.139423,0.0275521,0.0190579,0.00829112,0.148679,0.0619003,0.140982,0.0982016,0.0528514,0.108057,0.188635,0.132577,0.081977,0.0948982,0.0415721,0.215492,0.0236364,0.0907212,0.143747,0.0933697,0.204953,0.00676561,0.0180314,0.208242,0.0665252,0.0844722,0.688181,0.0429682,0.120351,0.0667043,0.0964797,0.0246116,0.140039,0.184019,0.120917,0.0362416,0.0380166,0.18151,0.111283,0.121201,0.154071,0.0541794,0.0701653,0.0929951,0.198787,0.0384161,0.107455,0.212709,0.0783235,0.105572,0.0294301,0.0117644,0.108602,0.0759481,0.054569,0.0504887,0.352278,0.0600088,0.0860723,0.167053,0.378921,0.067678,0.089036,0.119383,0.00747605,0.0171177,0.0964936,0.0436945,0.0372495,0.00725252,0.0956287,0.0279481,0.0425,0.114846,0.0472875,0.0347684,0.064341,0.209032,0.608896,0.062747,0.000112328,0.0495878,0.0953825,0.00114029,0.0853887,0.00688504,0.58489,0.153631,0.0927458,0.27413,0.0574857,0.0422457,0.0105769,0.0370665,0.219088,0.0409286,0.0669887,0.338096,0.144217,0.269326,0.182599,0.000584565,0.149552,0.0176855,0.101221,0.0337525,0.0203386,0.0566549,0.139021,0.0838393,0.16671,0.214708,0.140123,0.0857827,0.102368,0.176912,0.0906875,0.0147934,0.0843604,0.134932,0.0595773,0.0748346,0.0572164,0.0227861,0.125792,0.108101,0.0648644,0.0553359,0.0330399,0.00395526,0.022776,0.127606,0.203923,0.155998,0.596561,0.0693171,0.0988228,0.00365114,0.0389418,0.120833,0.200647,0.143677,0.0174119,0.0265818,0.0427088,0.117549,0.0747594,0.228385,0.0516985,0.0337251,0.227719,0.0952829,0.116642,0.147788,0.273479,0.114283,0.0400322,0.127369,0.0403542,0.0547453,0.0172085,0.137725,0.12972,0.0541353,0.0799324,0.090079,0.140334,0.181817,0.178449,0.0356339,0.158844,0.122474,0.0274061,0.115574,0.0737247,0.118847,0.183031,0.0401756,0.0828697,0.173562,0.107145,0.187297,0.122935,0.0284396,0.112671,0.0470731,0.00314485,0.0602859,0.0676496,0.00624688,0.0893019,0.060398,0.0308319,0.0606036,0.136451,0.00360981,0.0413967,0.0121616,0.0229156,0.178359,0.0458667,0.104357,0.121154,0.1129,0.312578,0.169057,0.164202,0.100942,0.062995,0.10299,0.14193,0.0800546,0.15606,0.161026,0.0738599,0.126611,0.138852,0.085973,0.060453,0.059896,0.569726,0.384785,0.0418404,0.0765029,0.0959204,0.0931946,0.0472272,0.263087,0.163502,0.214803,0.0177645,0.348993,0.0983991,0.0830921,0.116283,0.136838,0.0815104,0.111647,0.372804,0.117027,0.159052,0.185164,0.01843,0.0980288,0.0980899,0.159674,0.107242,0.201859,0.0695832,0.21774,0.0619218,0.1751,0.163376,0.128096,0.0345133,0.0810678,0.0811639,0.0920653,0.118078,0.0755168,0.0429376,0.063292,0.254773,0.119261,0.0865903,0.0380459,0.130174,0.219944,0.355018,0.782949,0.635872,0.20128,0.823736,0.489965,0.335423,0.261644,0.0376513,0.446302,0.373681,0.309233,0.147559,0.0619618,0.0146881,0.329568,0.53472,0.0724671,0.271958,0.292154,0.0964816,0.39729,0.0582602,0.230901,0.187251,0.362792,0.181715,0.423979,0.109988,0.330894,0.218329,0.427027,0.0821552,0.463191,0.647576,0.528324,0.168255,0.370782,0.415647,0.484505,0.253571,0.0424424,0.301787,0.481778,0.316882,0.0270783,0.503224,0.603208,0.283727,0.314747,0.577664,0.0474194,0.120054,0.576651,0.416816,0.0478086,0.476744,0.439556,0.0807167,0.056723,0.241757,0.18237,0.706298,0.513427,0.747852,0.0419647,0.236471,0.185661,0.346319,0.179399,0.00415948,0.625945,0.503058,0.513852,0.169228,0.248634,0.281576,0.472384,0.163244,0.0670502,0.0730934,0.184794,0.230427,0.762864,0.581837,0.412837,0.671377,0.546839,0.191921,0.448039,0.218623,0.312808,0.333034,0.0451077,0.0747529,0.229003,0.650179,0.589326,0.50215,0.294698,0.34331,0.477304,0.289204,0.327108,0.683186,0.0428373,0.490301,0.428671,0.228096,0.336314,0.0209597,0.15631,0.567452,0.421464,0.48267,0.420626,0.165111,0.311758,0.0637439,0.144809,0.0111455,0.385517,0.376191,0.447325,0.127215,0.0348837,0.0122989,0.0465712,0.00985947,0.259235,0.134788,0.0985856,0.546222,0.293698,0.284593,0.343734,0.0526965,0.305777,0.601433,0.503082,0.169823,0.00488238,0.262537,0.359455,0.226257,0.405955,0.41707,0.363685,0.130283,0.753577,0.0228979,0.171685,0.284166,0.437176,0.269226,0.339277,0.192529,0.281425,0.0105593,0.455379,0.520495,0.159617,0.238587,0.372281,0.232251,0.0192138,0.0891382,0.0595618,0.171389,0.257493,0.347298,0.539392,0.34988,0.136757,0.0958562,0.273024,0.0793778,0.316179,0.0697683,0.0556835,0.192544,0.0779981,0.0575676,0.144322,0.0270501,0.203656,0.116981,0.441735,0.191777,0.111931,0.28934,0.0435386,0.00601662,0.126478,0.134852,0.10689,0.273326,0.0627924,0.381386,0.0179103,0.303939,0.279795,0.390395,0.0464827,0.169603,0.114583,0.104559,0.0899537,0.0866966,0.15983,0.107111,0.0438639,0.00389058,0.00797323,0.129156,0.210369,0.193675,0.00934729,0.0499762,0.0828956,0.0666953,0.182185,0.111277,0.219383,0.332809,0.19559,0.132201,0.188694,0.0481795,0.199971,0.406014,0.127758,0.175785,0.184486,0.169234,0.0876426,0.0952322,0.0112557,0.222432,0.00594521,0.0043762,0.00481323,0.173708,0.141119,0.211595,0.0300692,0.131551,0.0445237,0.052362,0.208866,0.0123828,0.0797897,0.0974211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}}
}}

Revision as of 14:54, 19 October 2012


Full id: C3218_CD14_Neutrophils_Eosinophils_Peripheral_Monocytederived_CD19_parietal



Phase1 CAGE Peaks

Hg19::chr12:10277776..10277780,-p@chr12:10277776..10277780
-
Hg19::chr5:17221493..17221497,+p@chr5:17221493..17221497
+
Hg19::chr6:15246501..15246524,+p12@JARID2


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
myeloid leukocyte3.36e-4972
granulocyte monocyte progenitor cell1.21e-4367
macrophage dendritic cell progenitor2.79e-4361
monopoietic cell3.99e-4259
monocyte3.99e-4259
monoblast3.99e-4259
promonocyte3.99e-4259
defensive cell1.37e-4148
phagocyte1.37e-4148
myeloid lineage restricted progenitor cell1.95e-4166
classical monocyte1.47e-3942
CD14-positive, CD16-negative classical monocyte1.47e-3942
leukocyte1.90e-35136
hematopoietic lineage restricted progenitor cell5.24e-30120
nongranular leukocyte6.63e-30115
myeloid cell5.04e-29108
common myeloid progenitor5.04e-29108
hematopoietic stem cell2.43e-24168
angioblastic mesenchymal cell2.43e-24168
hematopoietic oligopotent progenitor cell7.72e-24161
hematopoietic multipotent progenitor cell7.72e-24161
hematopoietic cell2.06e-23177
stuff accumulating cell1.10e-1787
intermediate monocyte5.22e-099
CD14-positive, CD16-positive monocyte5.22e-099
Uber Anatomy
Ontology termp-valuen
hematopoietic system1.97e-3998
blood island1.97e-3998
bone marrow8.06e-3876
bone element6.70e-3682
hemolymphoid system7.53e-35108
skeletal element2.44e-3090
immune system4.21e-3093
skeletal system6.04e-29100
musculoskeletal system1.48e-11167
lateral plate mesoderm3.69e-10203


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
FAM48A#555781385.056250.002594789661407470.0143491071400897



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.