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Coexpression cluster:C2534: Difference between revisions

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|tf_chipseq_enrich=BCL11A#53335;4:28.3694551036071:1.542446414682e-06:5.89431251748897e-05!EBF1#1879;4:8.906466846569:0.0001588790747201:0.00199677156253821!MAX#4149;4:6.45255550900712:0.000576761319564549:0.00485542281589569!MYC#4609;4:5.2222818716094:0.00134430939527274:0.0088792264693201!NFKB1#4790;4:5.48806342419384:0.00110219956630198:0.00768083142089893!PAX5#5079;4:6.66956553117783:0.000505277416948326:0.00444010670161264!TBP#6908;4:3.70677068709639:0.00529637781478435:0.0244345084635685!TCF12#6938;4:10.6344649021864:7.8163066689251e-05:0.00120101111107234
|tf_chipseq_enrich=BCL11A#53335;4:28.3694551036071:1.542446414682e-06:5.89431251748897e-05!EBF1#1879;4:8.906466846569:0.0001588790747201:0.00199677156253821!MAX#4149;4:6.45255550900712:0.000576761319564549:0.00485542281589569!MYC#4609;4:5.2222818716094:0.00134430939527274:0.0088792264693201!NFKB1#4790;4:5.48806342419384:0.00110219956630198:0.00768083142089893!PAX5#5079;4:6.66956553117783:0.000505277416948326:0.00444010670161264!TBP#6908;4:3.70677068709639:0.00529637781478435:0.0244345084635685!TCF12#6938;4:10.6344649021864:7.8163066689251e-05:0.00120101111107234
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}}
}}

Revision as of 15:34, 26 November 2012


Full id: C2534_Basophils_CD14_Natural_CD14CD16_Whole_acute_blood



Phase1 CAGE Peaks

Hg19::chr1:160832534..160832564,-p2@CD244
Hg19::chr1:160832568..160832579,-p4@CD244
Hg19::chr1:160832600..160832618,-p3@CD244
Hg19::chr1:160832642..160832653,-p5@CD244


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>disease_data<br>


Cell Type
Ontology termp-valuen
hematopoietic stem cell8.37e-75168
angioblastic mesenchymal cell8.37e-75168
hematopoietic oligopotent progenitor cell4.36e-71161
hematopoietic multipotent progenitor cell4.36e-71161
hematopoietic cell5.21e-69177
myeloid cell2.74e-64108
common myeloid progenitor2.74e-64108
nongranular leukocyte6.19e-54115
leukocyte6.43e-53136
classical monocyte1.65e-5142
CD14-positive, CD16-negative classical monocyte1.65e-5142
hematopoietic lineage restricted progenitor cell2.72e-50120
defensive cell4.13e-4948
phagocyte4.13e-4948
monopoietic cell1.67e-4859
monocyte1.67e-4859
monoblast1.67e-4859
promonocyte1.67e-4859
macrophage dendritic cell progenitor1.67e-4861
myeloid leukocyte1.08e-4572
myeloid lineage restricted progenitor cell7.30e-4566
granulocyte monocyte progenitor cell2.83e-4467
stuff accumulating cell2.70e-1987
mesenchymal cell3.29e-16354
connective tissue cell2.93e-15361
intermediate monocyte2.28e-129
CD14-positive, CD16-positive monocyte2.28e-129
motile cell5.50e-12386
CD8-positive, alpha-beta T cell7.87e-1211
T cell3.95e-1025
pro-T cell3.95e-1025
nucleate cell8.58e-1055
lymphoid lineage restricted progenitor cell5.01e-0952
lymphocyte1.03e-0853
common lymphoid progenitor1.03e-0853
mature alpha-beta T cell1.95e-0818
alpha-beta T cell1.95e-0818
immature T cell1.95e-0818
mature T cell1.95e-0818
immature alpha-beta T cell1.95e-0818
stem cell2.96e-08441
multi fate stem cell3.38e-08427
somatic stem cell1.06e-07433
Uber Anatomy
Ontology termp-valuen
hematopoietic system4.61e-5298
blood island4.61e-5298
hemolymphoid system1.09e-47108
bone marrow2.43e-3876
immune system8.35e-3893
bone element4.69e-3482
skeletal element2.93e-2990
skeletal system2.17e-24100
lateral plate mesoderm8.49e-15203
connective tissue2.00e-14371
blood1.86e-1015
haemolymphatic fluid1.86e-1015
organism substance1.86e-1015
musculoskeletal system3.19e-09167
adult organism7.80e-07114
Disease
Ontology termp-valuen
myeloid leukemia1.82e-1831
leukemia5.70e-1839
hematologic cancer1.33e-1551
immune system cancer1.33e-1551


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#53335428.36945510360711.542446414682e-065.89431251748897e-05
EBF1#187948.9064668465690.00015887907472010.00199677156253821
MAX#414946.452555509007120.0005767613195645490.00485542281589569
MYC#460945.22228187160940.001344309395272740.0088792264693201
NFKB1#479045.488063424193840.001102199566301980.00768083142089893
PAX5#507946.669565531177830.0005052774169483260.00444010670161264
TBP#690843.706770687096390.005296377814784350.0244345084635685
TCF12#6938410.63446490218647.8163066689251e-050.00120101111107234



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.