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Coexpression cluster:C476: Difference between revisions

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|tf_chipseq_enrich=GATA3#2625;4:5.4473032714412:0.00548679388819938:0.0248465189649939!USF1#7391;8:2.54459971088318:0.00789784815901673:0.032420539418267
|tf_chipseq_enrich=GATA3#2625;4:5.4473032714412:0.00548679388819938:0.0248465189649939!USF1#7391;8:2.54459971088318:0.00789784815901673:0.032420539418267
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|tfbs_overrepresentation_for_novel_motifs=0.111472,1.58615,0.348202,0.577617,0.601808,0.574869,0.253108,0.0345625,0.31878,0.567121,0.177199,0.286323,0.718946,0.244498,0.285984,0.319274,0.43322,0.214415,0.105136,0.755249,0.707996,0.471127,0.561949,0.280777,0.134089,0.304148,1.29742,0.558352,0.609533,0.559665,0.162709,0.465029,0.174335,0.0955518,0.240789,0.590828,0.0667305,0.576802,1.20345,0.832619,0.238949,0.463281,0.354107,0.594631,0.24565,0.125045,0.706544,0.169954,0.491295,0.609855,0.315441,0.262847,0.403678,0.532773,0.671855,0.246686,0.620478,0.222594,0.0630426,0.631782,0.500944,0.255713,0.917082,0.409576,0.269358,0.380605,0.754286,1.10771,0.456006,0.950487,0.143869,0.953411,0.036434,0.670004,0.020227,0.390082,0.586496,0.395294,0.45319,0.408148,0.497004,0.408665,0.269087,0.939757,0.622646,0.0261694,0.315868,0.0595657,1.60354,1.20481,0.84263,0.598,1.20603,0.409701,0.288936,0.199002,0.477063,0.517267,0.340143,0.275452,0.208183,0.474756,1.27572,0.436368,0.371019,0.174162,0.422802,0.241933,0.133935,0.0770225,0.364924,0.509866,0.693651,1.63382,0.797061,0.23451,0.0851163,0.487455,0.378653,0.73226,0.662347,0.334429,0.195973,0.277756,0.90249,0.395934,0.248345,0.484077,0.701879,0.442144,1.45828,0.494009,0.715286,0.275188,0.854902,0.148502,0.158817,0.55929,0.814541,1.65405,1.25623,0.779227,0.249639,0.514137,0.372477,0.216494,0.35869,1.49614,0.150069,0.402254,0.0912904,0.0402223,0.598976,0.0312069,0.255347,0.980005,1.55723,0.56727,0.134125,0.37363,0.77808,0.582159,0.452507,0.760235,0.385896,1.35872,1.03727,0.252107,0.782314
}}
}}

Revision as of 14:14, 26 November 2012


Full id: C476_thymus_acute_Hodgkin_CD4_CD8_chronic_vein



Phase1 CAGE Peaks

Hg19::chr11:118209551..118209563,+p@chr11:118209551..118209563
+
Hg19::chr11:128344618..128344625,-p@chr11:128344618..128344625
-
Hg19::chr12:56324854..56324865,+p8@DGKA
Hg19::chr17:37309243..37309269,-p3@PLXDC1
Hg19::chr17:37309281..37309308,-p4@PLXDC1
Hg19::chr20:31097697..31097710,+p3@AK097865
Hg19::chr20:31097722..31097734,+p2@AK097865
Hg19::chr21:44597363..44597380,+p@chr21:44597363..44597380
+
Hg19::chr2:87036803..87036819,+p@chr2:87036803..87036819
+
Hg19::chr5:133450223..133450240,-p@chr5:133450223..133450240
-
Hg19::chr5:133451159..133451187,-p@chr5:133451159..133451187
-
Hg19::chr5:133451190..133451218,-p@chr5:133451190..133451218
-
Hg19::chr5:133451294..133451310,+p2@TCF7
Hg19::chr6:166825362..166825375,+p@chr6:166825362..166825375
+
Hg19::chr6:25442306..25442342,+p@chr6:25442306..25442342
+
Hg19::chr7:141998704..141998722,+p1@TRBV1
Hg19::chr7:55543402..55543436,+p@chr7:55543402..55543436
+
Hg19::chrX:123870889..123870903,-p@chrX:123870889..123870903
-
Hg19::chrX:123870918..123870949,-p@chrX:123870918..123870949
-
Hg19::chrX:123870951..123870959,-p@chrX:123870951..123870959
-


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
mature alpha-beta T cell1.85e-5418
alpha-beta T cell1.85e-5418
immature T cell1.85e-5418
mature T cell1.85e-5418
immature alpha-beta T cell1.85e-5418
T cell1.53e-4225
pro-T cell1.53e-4225
CD8-positive, alpha-beta T cell1.91e-3811
lymphoid lineage restricted progenitor cell5.62e-2552
lymphocyte2.12e-2453
common lymphoid progenitor2.12e-2453
nucleate cell2.59e-2355
CD4-positive, alpha-beta T cell5.30e-216
nongranular leukocyte7.62e-14115
leukocyte6.87e-12136
naive T cell3.12e-113
single nucleate cell8.21e-113
mononuclear cell8.21e-113
natural killer cell9.73e-113
pro-NK cell9.73e-113
hematopoietic lineage restricted progenitor cell1.23e-09120
hematopoietic stem cell1.98e-08168
angioblastic mesenchymal cell1.98e-08168
regulatory T cell6.90e-082
CD4-positive, CD25-positive, alpha-beta regulatory T cell6.90e-082
naive regulatory T cell6.90e-082
hematopoietic cell1.08e-07177
Uber Anatomy
Ontology termp-valuen
blood5.14e-2115
haemolymphatic fluid5.14e-2115
organism substance5.14e-2115
hemopoietic organ1.46e-127
immune organ1.46e-127
thymus3.09e-094
hemolymphoid system gland3.09e-094
thymic region3.09e-094
pharyngeal gland3.09e-094
thymus primordium3.09e-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)

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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
GATA3#262545.44730327144120.005486793888199380.0248465189649939
USF1#739182.544599710883180.007897848159016730.032420539418267



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.