Personal tools

Coexpression cluster:C3069

From FANTOM5_SSTAR

Revision as of 15:55, 12 September 2012 by Autoedit (talk | contribs)
Jump to: navigation, search


Full id: C3069_CD19_Eosinophils_CD4_CD8_Natural_Peripheral_CD14



Phase1 CAGE Peaks

Hg19::chr11:102188378..102188394,+p@chr11:102188378..102188394
+
Hg19::chr2:136890178..136890205,+p@chr2:136890178..136890205
+
Hg19::chr7:7855944..7855956,+p@chr7:7855944..7855956
+


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
leukocyte1.02e-70140
hematopoietic stem cell2.86e-57172
angioblastic mesenchymal cell2.86e-57172
hematopoietic cell6.97e-56182
hematopoietic lineage restricted progenitor cell3.30e-53124
nongranular leukocyte6.12e-53119
hematopoietic oligopotent progenitor cell9.20e-52165
hematopoietic multipotent progenitor cell9.20e-52165
lymphoid lineage restricted progenitor cell7.25e-3752
lymphocyte7.49e-3653
common lymphoid progenitor7.49e-3653
CD14-positive, CD16-negative classical monocyte7.20e-2742
classical monocyte1.17e-2545
myeloid leukocyte3.74e-2476
myeloid cell6.28e-19112
common myeloid progenitor6.28e-19112
lymphocyte of B lineage1.06e-1824
pro-B cell1.06e-1824
granulocyte monocyte progenitor cell1.57e-1871
macrophage dendritic cell progenitor3.81e-1765
myeloid lineage restricted progenitor cell1.51e-1670
mature alpha-beta T cell3.33e-1618
alpha-beta T cell3.33e-1618
immature T cell3.33e-1618
mature T cell3.33e-1618
immature alpha-beta T cell3.33e-1618
T cell1.03e-1525
pro-T cell1.03e-1525
monopoietic cell1.35e-1563
monocyte1.35e-1563
monoblast1.35e-1563
promonocyte1.35e-1563
B cell2.51e-1514
mesenchymal cell4.54e-14358
connective tissue cell3.34e-13365
intermediate monocyte5.27e-119
CD14-positive, CD16-positive monocyte5.27e-119
CD8-positive, alpha-beta T cell1.26e-1011
motile cell3.15e-10390
granulocyte3.45e-108
CD4-positive, alpha-beta T cell1.33e-086
blood cell2.26e-0811
stem cell2.70e-07444
multi fate stem cell3.37e-07430
circulating cell4.79e-076
somatic stem cell9.68e-07436
Uber Anatomy
Ontology termp-valuen
hematopoietic system5.02e-24102
blood island5.02e-24102
hemolymphoid system4.26e-22112
bone marrow7.92e-1680
bone element8.48e-1486
immune system7.22e-13115
connective tissue1.87e-12375
skeletal element1.78e-10101
skeletal system1.78e-10101


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
BCL11A#53335328.36945510360714.37778126761649e-050.000776513413397755
IRF4#3662321.91451268674419.49854535978121e-050.00136004740722538
MEF2A#4205318.74323090964410.0001518243905622470.00194771987789344
MEF2C#4208227.54090299508270.001729119938369690.0106453405590304
NFKB1#479035.488063424193840.006049381815655430.0268573111479866
PAX5#507936.669565531177830.003370290999677260.0172256935360328
POU2F2#545239.106124057742520.001324165192682130.00879400283343056
SMC3#9126210.02995522995520.0126656379767470.045706318532652
SPI1#668838.204323508522730.001810593189410520.010880123251372



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.