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Coexpression cluster:C1618: Difference between revisions

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|tf_chipseq_enrich=EGR1#1958;5:4.98817909481014:0.000323739800059071:0.00330347444830184!GATA1#2623;5:13.5603081438004:2.17950082879909e-06:7.83023347296003e-05!GATA2#2624;5:12.744931733554:2.9719152914525e-06:0.000101036413126305!PBX3#5090;5:21.9145126867441:1.97628413609567e-07:1.06999035194243e-05!TAL1#6886;5:29.8686166774402:4.19996766955644e-08:2.76395982004288e-06
|tf_chipseq_enrich=EGR1#1958;5:4.98817909481014:0.000323739800059071:0.00330347444830184!GATA1#2623;5:13.5603081438004:2.17950082879909e-06:7.83023347296003e-05!GATA2#2624;5:12.744931733554:2.9719152914525e-06:0.000101036413126305!PBX3#5090;5:21.9145126867441:1.97628413609567e-07:1.06999035194243e-05!TAL1#6886;5:29.8686166774402:4.19996766955644e-08:2.76395982004288e-06
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}}
}}

Revision as of 15:00, 26 November 2012


Full id: C1618_mycosis_CD4_thymus_CD8_Natural_chronic_Basophils



Phase1 CAGE Peaks

Hg19::chr11:12217457..12217477,+p3@MICAL2
Hg19::chr11:12217480..12217534,+p2@MICAL2
Hg19::chr11:12217537..12217545,+p26@MICAL2
Hg19::chr11:12217551..12217561,+p22@MICAL2
Hg19::chr11:12217563..12217573,+p28@MICAL2


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
T cell8.11e-4425
pro-T cell8.11e-4425
mature alpha-beta T cell6.19e-3518
alpha-beta T cell6.19e-3518
immature T cell6.19e-3518
mature T cell6.19e-3518
immature alpha-beta T cell6.19e-3518
CD8-positive, alpha-beta T cell7.68e-3211
lymphoid lineage restricted progenitor cell1.13e-2952
lymphocyte5.59e-2953
common lymphoid progenitor5.59e-2953
nucleate cell1.14e-2755
leukocyte2.03e-18136
circulating cell8.74e-176
nongranular leukocyte2.39e-16115
hematopoietic cell5.02e-16177
hematopoietic stem cell3.70e-14168
angioblastic mesenchymal cell3.70e-14168
hematopoietic lineage restricted progenitor cell7.11e-12120
hematopoietic oligopotent progenitor cell3.73e-11161
hematopoietic multipotent progenitor cell3.73e-11161
natural killer cell2.62e-103
pro-NK cell2.62e-103
single nucleate cell2.64e-093
mononuclear cell2.64e-093
CD4-positive, alpha-beta T cell2.40e-086
Uber Anatomy
Ontology termp-valuen
blood5.98e-1115
haemolymphatic fluid5.98e-1115
organism substance5.98e-1115
hemopoietic organ1.06e-107
immune organ1.06e-107
thymus6.28e-084
hemolymphoid system gland6.28e-084
thymic region6.28e-084
pharyngeal gland6.28e-084
thymus primordium6.28e-084


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
EGR1#195854.988179094810140.0003237398000590710.00330347444830184
GATA1#2623513.56030814380042.17950082879909e-067.83023347296003e-05
GATA2#2624512.7449317335542.9719152914525e-060.000101036413126305
PBX3#5090521.91451268674411.97628413609567e-071.06999035194243e-05
TAL1#6886529.86861667744024.19996766955644e-082.76395982004288e-06



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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