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Coexpression cluster:C4097: Difference between revisions

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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C4097_Neutrophils_Mast_Eosinophils_Macrophage_CD4_acute_Whole
|full_id=C4097_Neutrophils_Mast_Eosinophils_Macrophage_CD4_acute_Whole
|id=C4097
|id=C4097

Revision as of 17:08, 12 September 2012


Full id: C4097_Neutrophils_Mast_Eosinophils_Macrophage_CD4_acute_Whole



Phase1 CAGE Peaks

Hg19::chr22:37640236..37640252,-p2@RAC2
Hg19::chr22:37640254..37640276,-p3@RAC2
Hg19::chr22:37640277..37640327,-p1@RAC2


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 cell3.57e-58172
angioblastic mesenchymal cell3.57e-58172
hematopoietic cell2.33e-56182
hematopoietic oligopotent progenitor cell1.24e-54165
hematopoietic multipotent progenitor cell1.24e-54165
leukocyte1.14e-46140
hematopoietic lineage restricted progenitor cell1.07e-40124
nongranular leukocyte4.17e-40119
myeloid cell3.13e-30112
common myeloid progenitor3.13e-30112
myeloid leukocyte9.06e-2476
lymphocyte6.02e-2253
common lymphoid progenitor6.02e-2253
lymphoid lineage restricted progenitor cell1.02e-2152
myeloid lineage restricted progenitor cell3.30e-1970
granulocyte monocyte progenitor cell6.80e-1971
multi fate stem cell3.01e-18430
somatic stem cell6.55e-18436
mesenchymal cell1.98e-17358
stem cell5.36e-17444
connective tissue cell1.13e-16365
monopoietic cell1.55e-1663
monocyte1.55e-1663
monoblast1.55e-1663
promonocyte1.55e-1663
macrophage dendritic cell progenitor5.88e-1665
CD14-positive, CD16-negative classical monocyte6.40e-1642
somatic cell2.13e-14591
classical monocyte1.28e-1245
T cell6.87e-1225
pro-T cell6.87e-1225
native cell3.86e-10722
lymphocyte of B lineage5.97e-1024
pro-B cell5.97e-1024
motile cell9.55e-10390
mature alpha-beta T cell2.11e-0918
alpha-beta T cell2.11e-0918
immature T cell2.11e-0918
mature T cell2.11e-0918
immature alpha-beta T cell2.11e-0918
B cell5.74e-0714
endothelial cell6.80e-0735
endothelial cell of vascular tree7.36e-0724
Uber Anatomy
Ontology termp-valuen
hemolymphoid system2.54e-31112
hematopoietic system6.13e-28102
blood island6.13e-28102
lateral plate mesoderm1.10e-27216
bone marrow3.97e-1880
immune system7.40e-18115
connective tissue1.65e-15375
bone element3.45e-1486
cardiovascular system8.08e-12110
circulatory system3.87e-11113
skeletal element2.60e-10101
skeletal system2.60e-10101
vessel1.56e-0969
musculoskeletal system2.82e-09167
blood2.73e-0815
haemolymphatic fluid2.73e-0815
organism substance2.73e-0815
blood vessel2.45e-0760
epithelial tube open at both ends2.45e-0760
blood vasculature2.45e-0760
vascular cord2.45e-0760
splanchnic layer of lateral plate mesoderm2.71e-0784
vasculature6.63e-0779
vascular system6.63e-0779
Disease
Ontology termp-valuen
hematologic cancer2.89e-1551
immune system cancer2.89e-1551
leukemia4.64e-1339
myeloid leukemia1.12e-1031


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
E2F6#187635.017155731697390.00791769806886330.0322976396755854
EBF1#187938.9064668465690.00141523283560980.00916566427621557
EGR1#195834.988179094810140.008056488137383440.0321223014652283
ELF1#199734.258097958807540.01295179875054610.0463260012229283
ETS1#211339.728760922202340.001085840092584840.00763560822983219
FOS#235338.99795530889440.001372499272417130.00898867821608908
GABPB1#255337.067683836182170.002832212825417420.0154388786092056
IRF1#365937.63716375356390.002244692747297240.0128330121433642
MAX#414936.452555509007120.003721913834265510.0186899201335155
MYC#460935.22228187160940.007020843755740150.0295058509116633
NFKB1#479035.488063424193840.006049381815655430.0270030938772166
PAX5#507936.669565531177830.003370290999677260.0173197766921859
PBX3#5090321.91451268674419.49854535978121e-050.00136867905467741
POU2F2#545239.106124057742520.001324165192682130.0088338862062299
SIN3A#2594235.408884726815140.006318961977991520.0277334875617522
SPI1#668838.204323508522730.001810593189410520.0109222285051028
TCF12#6938310.63446490218640.0008313523990202070.00630130003637937
ZBTB7A#5134137.35190930787590.002516255860282270.0140502163062457



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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