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Coexpression cluster:C1420: Difference between revisions

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|tf_chipseq_enrich=THAP1#55145;3:15.6845723014257:0.000602346980086485:0.00503147374656102!USF1#7391;4:4.24099951813864:0.00700536775082942:0.0296040140215616!ZBTB7A#51341;4:4.90127287191726:0.00407962811884375:0.0194873893662606
|tf_chipseq_enrich=THAP1#55145;3:15.6845723014257:0.000602346980086485:0.00503147374656102!USF1#7391;4:4.24099951813864:0.00700536775082942:0.0296040140215616!ZBTB7A#51341;4:4.90127287191726:0.00407962811884375:0.0194873893662606
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|tfbs_overrepresentation_for_novel_motifs=0.44418,0.603698,0.436508,0.58616,0.393082,0.584466,0.662701,0.269608,0.267027,0.075749,0.553339,0.707204,1.18908,0.650887,0.391663,1.06849,0.889639,0.892779,0.236034,0.127969,0.436569,0.6169,0.576478,1.00694,0.483957,0.730467,0.202389,0.574247,1.02557,0.547818,0.530785,0.92701,0.816912,0.640661,0.35719,0.316592,0.35388,0.585658,0.329602,0.69481,0.355745,0.513952,0.323162,0.390088,0.992846,0.468392,0.66382,1.33909,0.630853,0.396429,0.745008,0.675919,0.455399,1.00488,1.15929,0.653901,1.03549,0.62023,0.186533,0.619193,0.968558,0.666252,0.267534,0.861462,0.684675,0.826413,1.24834,1.61834,0.916468,1.45553,0.500342,1.38456,0.146905,1.15727,0.218784,0.594475,1.07049,0.84426,0.913168,1.20149,1.25579,0.86037,0.684313,0.749276,1.10535,0.0481066,0.126687,0.181871,0.771626,1.71797,1.34233,1.07807,0.94406,0.30974,0.393853,0.32338,0.661488,0.987239,0.776336,0.498077,0.330999,0.938327,0.981588,0.893363,0.814675,0.548668,0.877269,0.647343,0.483695,0.376529,1.13818,0.978783,0.430775,0.563054,1.29401,0.352243,0.460936,0.529546,0.824029,0.312699,1.14892,0.769145,0.581628,0.695878,1.40534,0.845034,0.656181,0.949126,1.1919,0.324369,1.07876,0.53374,1.20639,0.692462,1.35529,0.999497,0.524606,0.57483,1.31259,2.17352,1.7705,1.27501,0.657956,0.983666,0.816466,0.611524,0.799467,2.01411,0.510514,0.306342,0.424432,0.0926553,1.07915,0.258882,0.665754,1.48627,0.755083,0.378604,0.484017,0.454152,1.27379,1.06043,0.912368,0.457485,0.83286,0.683502,0.29379,0.661335,1.11626
}}
}}

Revision as of 14:52, 26 November 2012


Full id: C1420_CD4_acute_Hodgkin_chronic_thymus_CD8_Whole



Phase1 CAGE Peaks

Hg19::chr16:30390783..30390810,-p@chr16:30390783..30390810
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Hg19::chr7:142498799..142498808,+p5@AJ568018
Hg19::chr7:142498836..142498876,-p@chr7:142498836..142498876
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Hg19::chr7:142498988..142499010,-p@chr7:142498988..142499010
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Hg19::chr7:142499055..142499068,-p@chr7:142499055..142499068
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Hg19::chr7:142499841..142499860,-p@chr7:142499841..142499860
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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
lymphocyte3.28e-4853
common lymphoid progenitor3.28e-4853
lymphoid lineage restricted progenitor cell1.31e-4652
nucleate cell4.98e-4655
T cell5.04e-4625
pro-T cell5.04e-4625
mature alpha-beta T cell1.12e-3618
alpha-beta T cell1.12e-3618
immature T cell1.12e-3618
mature T cell1.12e-3618
immature alpha-beta T cell1.12e-3618
CD8-positive, alpha-beta T cell8.31e-2311
nongranular leukocyte1.02e-20115
leukocyte5.47e-18136
hematopoietic lineage restricted progenitor cell6.95e-15120
CD4-positive, alpha-beta T cell1.17e-136
hematopoietic cell2.04e-13177
hematopoietic stem cell4.01e-13168
angioblastic mesenchymal cell4.01e-13168
hematopoietic oligopotent progenitor cell9.83e-11161
hematopoietic multipotent progenitor cell9.83e-11161
circulating cell2.51e-086
naive T cell1.17e-073
natural killer cell3.47e-073
pro-NK cell3.47e-073
single nucleate cell5.51e-073
mononuclear cell5.51e-073
Uber Anatomy
Ontology termp-valuen
blood1.05e-1715
haemolymphatic fluid1.05e-1715
organism substance1.05e-1715
hemopoietic organ9.81e-117
immune organ9.81e-117
thymus1.30e-094
hemolymphoid system gland1.30e-094
thymic region1.30e-094
pharyngeal gland1.30e-094
thymus primordium1.30e-094


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
THAP1#55145315.68457230142570.0006023469800864850.00503147374656102
USF1#739144.240999518138640.007005367750829420.0296040140215616
ZBTB7A#5134144.901272871917260.004079628118843750.0194873893662606



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.