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Coexpression cluster:C741: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002371!4.54e-18!80;UBERON:0001474!3.53e-17!86;UBERON:0004765!1.20e-14!101;UBERON:0001434!1.20e-14!101;UBERON:0002390!2.53e-14!102;UBERON:0003061!2.53e-14!102;UBERON:0002193!2.08e-12!112;UBERON:0002405!7.96e-10!115;UBERON:0003081!3.33e-08!216
|ontology_enrichment_uberon=UBERON:0002371!4.54e-18!80;UBERON:0001474!3.53e-17!86;UBERON:0004765!1.20e-14!101;UBERON:0001434!1.20e-14!101;UBERON:0002390!2.53e-14!102;UBERON:0003061!2.53e-14!102;UBERON:0002193!2.08e-12!112;UBERON:0002405!7.96e-10!115;UBERON:0003081!3.33e-08!216
|tf_chipseq_enrich=EBF1#1879;5:4.04839402116773:0.00459238325242163:0.0217034216253976!FOS#2353;7:5.72597156020553:4.5912826243232e-05:0.000806982440258651!JUN#3725;6:6.82517955945618:8.44439089932034e-05:0.00126694977896009!NFKB1#4790;6:2.99348914046936:0.00728556496302957:0.0301405077906059!SMARCC2#6601;2:17.1191589867087:0.00581844647605355:0.0261533346895871!STAT3#6774;5:4.78157499870647:0.00219206266137762:0.0126358777067898!TBP#6908;7:2.35885407360679:0.011797348605664:0.0429783483684576
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92819,0.150458,0.560857,0.167908,0.505898,0.816691,0.116017,0.792481,0.597049,0.137272,0.201882,0.86367,0.380631,0.344691,0.000989973,0.670834,0.100939,0.946206,0.112945,0.135223,0.285057,0.187413,0.4347,0.657997,0.226519,0.0436001,0.0948532,0.840699,0.0788918,0.351879,0.0348088,0.50054,0.268916,0.169734,0.776021,0.443444,0.428369,0.488883,0.426313,0.289378,0.742922,0.710877,0.162791,0.306168,0.636157,0.407148,0.255865,0.345558,0.0147374,0.403546,0.925902,0.887401,0.17731,0.0572822,0.171564,0.208652,0.250155,0.000528624,0.112264,0.119189,0.246188,0.333658,0.548076,0.901226,0.592704,0.356157,0.372151,0.543363,0.512553,0.945549,0.195403,0.163718,0.839641,0.205682,0.506771,0.145413,0.237617,0.605162,0.716786,0.124403,0.388692,0.506277,0.999861,0.999959,0.571685,0.59446,0.343085,0.225589,0.344355,0.169548,0.308886,0.570254,0.25036,0.157465,0.348305,0.234465,0.609431,0.457137,0.131401,0.40648,0.155356,0.183897,0.359054,0.00584874,0.153701,0.334046,0.234391,0.194141,0.624261,0.251557,0.710509,0.454553,0.548455,0.59461,0.324886,0.765993,0.501626,0.198407,0.452722,0.211264,0.183569,0.445539,0.923874,0.462646,0.239328,0.297755,0.203718,0.435273,0.450432,0.313173,0.460799,0.495664,0.045885,0.417939,0.61307,0.0920533,0.71234,0.371665,0.274764,0.185244,0.356138,0.354821,0.531143,0.505578,0.306067,0.675126,0.650129,0.426094,0.319827,0.664512,0.330545,0.355935,0.0905574,0.490328,0.29423,0.832571,0.488206,0.535384,0.267489,0.173303,0.463673,0.159394,0.738271,0.200162,0.647172,0.51347,0.594531,0.250798,0.85307,0.971186,0.126073,0.85748,0.40264,0.150341,0.408977,0.862706,0.0916821,0.887595,0.301233,0.619107,0.327144,0.356608,0.816305,0.333301,0.887416,0.193611,0.0404952,0.80693,0.851919,0.102233,0.616892,0.891307,0.0193936,0.847289,0.541499,0.444651,0.921589,0.363021,0.288879,0.981974,0.86913,0.611154,0.501568,0.469213,0.833271,0.707165,0.728062,0.564079,0.521812,0.713781,0.481939,0.663958,0.712022,0.606215,0.426336,0.443153,0.204147,0.66554,0.885729,0.640351,0.912112,0.837695,0.715858,0.413083,0.137363,0.748777,0.892177,0.245111,0.838364,0.246732,0.919767,0.907367,0.975931,0.740361,0.789151,0.203442,0.559768,0.569953,0.7303,0.66279,0.149288,0.0754067,0.83006,0.463307,0.108479,0.857261,0.309722,0.0136397,0.477215,0.481099,0.61753,0.374787,0.346811,0.805341,0.402693,0.000968372,0.343212,0.804101,0.681572,0.0461237,0.497681,0.417126,0.549534,0.781361,0.859331,0.535996,0.509109,0.981753,0.313895,0.601724,0.861382,0.586901,0.081178,0.360055,0.392105,0.568435,0.647446,0.422014,0.983495,0.488066,0.194181,0.273305,0.752172,0.221762,0.506508,0.773368,0.0954294,0.75477,0.8545,0.811368,0.939529,0.837603,0.808854,0.627335,0.203552,0.689958,0.097417,0.0692357,0.795167,0.692997,0.510037,0.0470621,0.636412,0.00805074,0.738902,0.149217,0.715049,0.534679,0.732839,0.653388,0.00967281,0.389332,0.727995,0.598324,0.265874,0.552624,0.0445229,0.197592,0.850525,0.153709,0.895388,0.705416,0.806786,0.416713,0.845937,0.689775,0.501476,0.692595,0.831373,0.687906,0.804458,0.781736,0.554317,0.857142,0.535628,0.773188,0.519832,0.375731,0.0347359,0.0538163,0.509116,0.257235,0.33325,0.569392,0.118164,0.537498,0.666588,0.178611,0.239417,0.676428,0.138801,0.540379,0.479343,0.230569,0.574762,0.292558,0.000567376,0.486305,0.0927405,0.0997452,0.66105,0.573809,0.175433,0.515687,0.00866375,0.599595,0.603486,0.453128,0.049765,0.594113,0.555962,0.531493,0.382823,0.557694,0.114406,0.301747,0.384693,0.51672,0.0702006,0.698203,0.27961,0.402705,0.211738,0.647625,0.602291,0.225542,0.211908,0.679099,0.355997,0.438647,0.615425,0.477261,0.614558,0.492207,0.134057,0.22178,0.0169654,0.0130483,0.318365,0.200418,0.212024,0.0248566,0.374709,0.316768,0.0672589,0.201618,0.22457,0.468824,0.598491,0.549025,0.0860835,0.301787,0.740651,0.518267,0.134832,0.664008,0.0230232,0.592401,0.0857138,0.1723,0.173921,0.240646,0.665997,0.30562,0.566369,0.586083,0.573867,0.429354,0.544513,0.282789,0.363633,0.0683243,0.645073,0.501724,0.559644,0.424261,0.00927204,0.635262,0.025542,0.00195082,0.0249397,0.236385,0.49975,0.00614007,0.311923,0.563078,0.744036,0.7016,0.594401,0.269963,0.562934,0.338919,0.182919,0.183452,0.451616,0.257575,0.141393,0.183331,0.412879,0.305584,0.581258,0.533448,0.0758769,0.00799941,0.267192,0.315214,0.215792,0.379171,0.0249608,0.333105,0.222472,0.252354,0.0918167,0.00926835,0.152456,0.224382,0.291235,0.128266,0.0999451,0.567591,0.13961,0.351331,0.462987,0.429017,0.673635,0.661783,0.558985,0.611867,6.403e-05,0.0940159,0.0362701,0.705698,0.675667,0.404324,0.473851,0.208157,0.557233,0.12925,0.628144,0.763537,0.363221,0.228206,0.605083,0.0108218,0.0467444,0.540283,0.70279,0.705047,0.651673,0.482941,0.605877,0.302498,0.766699,0.608655,0.574325,0.30896,0.280668,0.75272,0.498751,0.133309,0.11203,0.236983,0.321769,0.323272,0.235951,0.508119,0.466029,0.224186,0.656486,0.570694,0.806913
}}
}}

Revision as of 11:45, 5 September 2012


Full id: C741_immature_CD14_Basophils_Peripheral_Mallassezderived_Astrocyte_renal



Phase1 CAGE Peaks

Hg19::chr11:62321495..62321531,-p@chr11:62321495..62321531
-
Hg19::chr11:62321782..62321794,+p@chr11:62321782..62321794
+
Hg19::chr14:65673392..65673400,+p@chr14:65673392..65673400
+
Hg19::chr16:85858477..85858488,+p@chr16:85858477..85858488
+
Hg19::chr16:85858491..85858507,+p@chr16:85858491..85858507
+
Hg19::chr17:29923862..29923868,-p@chr17:29923862..29923868
-
Hg19::chr20:47893707..47893719,-p@chr20:47893707..47893719
-
Hg19::chr2:27851106..27851120,+p2@GPN1
Hg19::chr3:71113123..71113139,+p@chr3:71113123..71113139
+
Hg19::chr3:71113153..71113163,+p@chr3:71113153..71113163
+
Hg19::chr6:32572606..32572629,+p@chr6:32572606..32572629
+


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
CD14-positive, CD16-negative classical monocyte6.76e-2742
classical monocyte1.24e-2545
leukocyte4.59e-21140
myeloid leukocyte1.81e-1976
macrophage dendritic cell progenitor2.45e-1865
granulocyte monocyte progenitor cell4.81e-1871
myeloid lineage restricted progenitor cell4.65e-1770
monopoietic cell4.84e-1763
monocyte4.84e-1763
monoblast4.84e-1763
promonocyte4.84e-1763
animal cell5.96e-16679
eukaryotic cell5.96e-16679
hematopoietic lineage restricted progenitor cell4.01e-15124
nongranular leukocyte4.98e-15119
somatic cell1.89e-14591
native cell4.31e-14722
hematopoietic stem cell6.13e-14172
angioblastic mesenchymal cell6.13e-14172
hematopoietic cell7.40e-13182
myeloid cell7.16e-12112
common myeloid progenitor7.16e-12112
hematopoietic oligopotent progenitor cell1.78e-11165
hematopoietic multipotent progenitor cell1.78e-11165
Uber Anatomy
Ontology termp-valuen
bone marrow4.54e-1880
bone element3.53e-1786
skeletal element1.20e-14101
skeletal system1.20e-14101
hematopoietic system2.53e-14102
blood island2.53e-14102
hemolymphoid system2.08e-12112
immune system7.96e-10115
lateral plate mesoderm3.33e-08216


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
EBF1#187954.048394021167730.004592383252421630.0217034216253976
FOS#235375.725971560205534.5912826243232e-050.000806982440258651
JUN#372566.825179559456188.44439089932034e-050.00126694977896009
NFKB1#479062.993489140469360.007285564963029570.0301405077906059
SMARCC2#6601217.11915898670870.005818446476053550.0261533346895871
STAT3#677454.781574998706470.002192062661377620.0126358777067898
TBP#690872.358854073606790.0117973486056640.0429783483684576



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.