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Coexpression cluster:C1389: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002390!4.85e-23!102;UBERON:0003061!4.85e-23!102;UBERON:0002371!3.90e-21!80;UBERON:0002193!1.65e-19!112;UBERON:0001474!2.15e-19!86;UBERON:0002405!1.16e-13!115;UBERON:0002384!3.33e-13!375;UBERON:0004765!1.61e-12!101;UBERON:0001434!1.61e-12!101
|ontology_enrichment_uberon=UBERON:0002390!4.85e-23!102;UBERON:0003061!4.85e-23!102;UBERON:0002371!3.90e-21!80;UBERON:0002193!1.65e-19!112;UBERON:0001474!2.15e-19!86;UBERON:0002405!1.16e-13!115;UBERON:0002384!3.33e-13!375;UBERON:0004765!1.61e-12!101;UBERON:0001434!1.61e-12!101
|tf_chipseq_enrich=MEF2A#4205;3:9.37161545482203:0.00268739994710391:0.0148016750910023!NFKB1#4790;4:3.65870894946256:0.0120792728901523:0.0438295932103886!RFX5#5993;3:6.02395541359755:0.00943790403633506:0.0356022993444628!TBP#6908;5:3.08897557258032:0.00664544827578693:0.0282867611866201
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}}
}}

Revision as of 13:16, 5 September 2012


Full id: C1389_immature_CD19_CD14_Basophils_migratory_Natural_CD4



Phase1 CAGE Peaks

Hg19::chr14:105281710..105281738,+p1@AY927492
Hg19::chr6:32636347..32636362,+p@chr6:32636347..32636362
+
Hg19::chr6:32636372..32636386,+p@chr6:32636372..32636386
+
Hg19::chr6:32636402..32636417,+p@chr6:32636402..32636417
+
Hg19::chr7:128786662..128786710,+p@chr7:128786662..128786710
+
Hg19::chr7:129133189..129133195,+p@chr7:129133189..129133195
+


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
leukocyte5.28e-56140
hematopoietic lineage restricted progenitor cell1.61e-45124
hematopoietic stem cell2.66e-45172
angioblastic mesenchymal cell2.66e-45172
hematopoietic cell1.13e-43182
nongranular leukocyte1.71e-43119
hematopoietic oligopotent progenitor cell7.23e-41165
hematopoietic multipotent progenitor cell7.23e-41165
myeloid leukocyte2.61e-2676
CD14-positive, CD16-negative classical monocyte1.10e-2542
classical monocyte1.37e-2545
granulocyte monocyte progenitor cell1.55e-2371
myeloid lineage restricted progenitor cell3.35e-2270
macrophage dendritic cell progenitor4.24e-2265
lymphoid lineage restricted progenitor cell1.07e-2052
monopoietic cell1.20e-2063
monocyte1.20e-2063
monoblast1.20e-2063
promonocyte1.20e-2063
myeloid cell2.43e-20112
common myeloid progenitor2.43e-20112
lymphocyte7.08e-2053
common lymphoid progenitor7.08e-2053
mesenchymal cell5.97e-15358
connective tissue cell8.69e-14365
lymphocyte of B lineage9.54e-1224
pro-B cell9.54e-1224
motile cell3.55e-11390
T cell2.15e-0825
pro-T cell2.15e-0825
dendritic cell2.59e-0810
B cell3.45e-0814
mature alpha-beta T cell4.71e-0818
alpha-beta T cell4.71e-0818
immature T cell4.71e-0818
mature T cell4.71e-0818
immature alpha-beta T cell4.71e-0818
intermediate monocyte6.12e-089
CD14-positive, CD16-positive monocyte6.12e-089
conventional dendritic cell6.42e-078
Uber Anatomy
Ontology termp-valuen
hematopoietic system4.85e-23102
blood island4.85e-23102
bone marrow3.90e-2180
hemolymphoid system1.65e-19112
bone element2.15e-1986
immune system1.16e-13115
connective tissue3.33e-13375
skeletal element1.61e-12101
skeletal system1.61e-12101


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
MEF2A#420539.371615454822030.002687399947103910.0148016750910023
NFKB1#479043.658708949462560.01207927289015230.0438295932103886
RFX5#599336.023955413597550.009437904036335060.0356022993444628
TBP#690853.088975572580320.006645448275786930.0282867611866201



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.