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Coexpression cluster:C1412: Difference between revisions

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|tf_chipseq_enrich=EBF1#1879;5:7.42205570547417:9.7002838805275e-05:0.00138004079580222!IRF4#3662;3:10.9572563433721:0.00171175344181094:0.0106896566437032!MEF2A#4205;5:15.61935909137:2.47611227471544e-06:8.73952990398803e-05!MEF2C#4208;3:20.655677246312:0.000268356349406041:0.00286602605334057!NFKB1#4790;5:4.5733861868282:0.0010219625937113:0.00724496004104087!POLR2A#5430;6:2.14745317655807:0.0101957067681878:0.0380214746541015!POU2F2#5452;5:7.58843671478544:8.70203885493171e-05:0.00129040499214853!SP1#6667;4:3.7989209187606:0.0105224661679851:0.0389479672568115!SPI1#6688;4:5.46954900568182:0.0026973005361414:0.0148428985032969!TAF1#6872;6:3.34304628574529:0.000716247428463562:0.0057312415860639!ZEB1#6935;4:11.2589546783626:0.000167270037980545:0.0020484891529843
|tf_chipseq_enrich=EBF1#1879;5:7.42205570547417:9.7002838805275e-05:0.00138004079580222!IRF4#3662;3:10.9572563433721:0.00171175344181094:0.0106896566437032!MEF2A#4205;5:15.61935909137:2.47611227471544e-06:8.73952990398803e-05!MEF2C#4208;3:20.655677246312:0.000268356349406041:0.00286602605334057!NFKB1#4790;5:4.5733861868282:0.0010219625937113:0.00724496004104087!POLR2A#5430;6:2.14745317655807:0.0101957067681878:0.0380214746541015!POU2F2#5452;5:7.58843671478544:8.70203885493171e-05:0.00129040499214853!SP1#6667;4:3.7989209187606:0.0105224661679851:0.0389479672568115!SPI1#6688;4:5.46954900568182:0.0026973005361414:0.0148428985032969!TAF1#6872;6:3.34304628574529:0.000716247428463562:0.0057312415860639!ZEB1#6935;4:11.2589546783626:0.000167270037980545:0.0020484891529843
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|tfbs_overrepresentation_for_novel_motifs=0.44418,0.143275,0.436508,0.58616,1.01854,0.584466,0.662701,0.269608,0.267027,0.555913,0.553339,0.707204,0.223349,0.650887,1.01544,1.06849,0.889639,0.336106,0.236034,0.402028,0.436569,0.29639,0.576478,1.78264,0.483957,0.730467,1.10781,0.574247,0.396295,0.547818,0.530785,0.92701,0.816912,0.225641,0.35719,0.134746,0.35388,0.585658,0.329602,0.248856,0.355745,0.513952,0.0979105,0.390088,1.41477,0.468392,0.66382,0.542147,1.56014,0.396429,0.745008,0.675919,0.149032,1.00488,1.15929,0.653901,0.400834,0.62023,0.186533,0.619193,0.968558,0.666252,0.267534,0.861462,0.684675,0.826413,1.24834,1.61834,0.916468,1.45553,0.500342,1.38456,0.45007,1.15727,1.17153,0.206105,0.192925,0.84426,0.913168,1.20149,0.240887,0.86037,0.684313,0.749276,1.10535,0.0481066,0.126687,0.181871,0.771626,1.71797,1.34233,1.07807,0.94406,0.30974,0.393853,0.32338,0.234532,0.987239,0.776336,1.53398,0.330999,0.938327,0.981588,0.893363,0.814675,0.548668,0.877269,0.647343,0.483695,0.376529,0.44815,0.978783,1.10061,0.563054,1.29401,0.352243,1.21803,0.529546,0.824029,0.312699,1.14892,0.769145,0.581628,0.695878,1.40534,0.845034,0.656181,0.949126,1.1919,0.866571,1.07876,0.53374,1.20639,0.692462,3.00512,0.175219,0.524606,0.57483,1.31259,2.17352,1.7705,1.27501,0.657956,0.983666,0.816466,0.611524,0.799467,2.01411,1.27188,0.306342,0.424432,0.0926553,1.07915,0.258882,0.665754,1.48627,0.755083,0.378604,0.484017,0.454152,1.27379,1.06043,0.912368,0.457485,0.83286,0.683502,0.29379,0.661335,1.11626
}}
}}

Revision as of 14:52, 26 November 2012


Full id: C1412_lymphangiectasia_xeroderma_B_b_splenic_myeloma_CD19



Phase1 CAGE Peaks

Hg19::chr15:78358512..78358549,-p6@TBC1D2B
Hg19::chr2:25643953..25643972,+p1@ENST00000352271
Hg19::chr5:150521192..150521229,-p3@ANXA6
Hg19::chr5:150521234..150521251,-p4@ANXA6
Hg19::chr5:150521260..150521277,-p5@ANXA6
Hg19::chr8:62010032..62010041,+p@chr8:62010032..62010041
+


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>disease_data<br>

Cell Type
Ontology termp-valuen
lymphocyte1.28e-5653
common lymphoid progenitor1.28e-5653
lymphoid lineage restricted progenitor cell1.52e-5452
nucleate cell3.91e-5455
lymphocyte of B lineage3.58e-4724
pro-B cell3.58e-4724
B cell5.33e-2914
leukocyte3.71e-26136
nongranular leukocyte2.98e-25115
hematopoietic lineage restricted progenitor cell6.77e-21120
hematopoietic stem cell9.85e-19168
angioblastic mesenchymal cell9.85e-19168
hematopoietic cell3.85e-18177
hematopoietic oligopotent progenitor cell8.04e-17161
hematopoietic multipotent progenitor cell8.04e-17161
T cell2.55e-1025
pro-T cell2.55e-1025
mature alpha-beta T cell2.41e-0818
alpha-beta T cell2.41e-0818
immature T cell2.41e-0818
mature T cell2.41e-0818
immature alpha-beta T cell2.41e-0818
Langerhans cell5.58e-085
single nucleate cell1.44e-073
mononuclear cell1.44e-073
natural killer cell6.13e-073
pro-NK cell6.13e-073
Uber Anatomy
Ontology termp-valuen
blood8.24e-1415
haemolymphatic fluid8.24e-1415
organism substance8.24e-1415
hemopoietic organ5.35e-127
immune organ5.35e-127
spleen2.47e-083
gastrointestinal system mesentery2.47e-083
stomach region2.47e-083
mesentery2.47e-083
gastrointestinal system serosa2.47e-083
mesentery of stomach2.47e-083
gut mesentery2.47e-083
dorsal mesentery2.47e-083
dorsal mesogastrium2.47e-083
peritoneal cavity2.47e-083
spleen primordium2.47e-083
Disease
Ontology termp-valuen
lymphoma1.70e-1410


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#187957.422055705474179.7002838805275e-050.00138004079580222
IRF4#3662310.95725634337210.001711753441810940.0106896566437032
MEF2A#4205515.619359091372.47611227471544e-068.73952990398803e-05
MEF2C#4208320.6556772463120.0002683563494060410.00286602605334057
NFKB1#479054.57338618682820.00102196259371130.00724496004104087
POLR2A#543062.147453176558070.01019570676818780.0380214746541015
POU2F2#545257.588436714785448.70203885493171e-050.00129040499214853
SP1#666743.79892091876060.01052246616798510.0389479672568115
SPI1#668845.469549005681820.00269730053614140.0148428985032969
TAF1#687263.343046285745290.0007162474284635620.0057312415860639
ZEB1#6935411.25895467836260.0001672700379805450.0020484891529843



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.

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