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Coexpression cluster:C3017: Difference between revisions

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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C3017_CD14_CD14CD16_Eosinophils_Mast_Neutrophils_Basophils_CD34
|full_id=C3017_CD14_CD14CD16_Eosinophils_Mast_Neutrophils_Basophils_CD34
|id=C3017
|id=C3017

Revision as of 15:52, 12 September 2012


Full id: C3017_CD14_CD14CD16_Eosinophils_Mast_Neutrophils_Basophils_CD34



Phase1 CAGE Peaks

Hg19::chr10:43633941..43633960,+p3@CSGALNACT2
Hg19::chr10:43633962..43633969,+p5@CSGALNACT2
Hg19::chr10:43633970..43633986,+p4@CSGALNACT2


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
leukocyte2.16e-34140
myeloid leukocyte1.50e-3276
granulocyte monocyte progenitor cell2.58e-2971
hematopoietic lineage restricted progenitor cell5.13e-29124
myeloid lineage restricted progenitor cell4.70e-2870
CD14-positive, CD16-negative classical monocyte8.82e-2842
nongranular leukocyte5.09e-27119
macrophage dendritic cell progenitor7.20e-2765
monopoietic cell7.80e-2663
monocyte7.80e-2663
monoblast7.80e-2663
promonocyte7.80e-2663
hematopoietic stem cell8.31e-25172
angioblastic mesenchymal cell8.31e-25172
classical monocyte7.28e-2445
hematopoietic cell8.97e-23182
hematopoietic oligopotent progenitor cell3.91e-22165
hematopoietic multipotent progenitor cell3.91e-22165
myeloid cell6.12e-19112
common myeloid progenitor6.12e-19112
mesenchymal cell1.71e-18358
connective tissue cell9.52e-18365
multi fate stem cell5.60e-16430
somatic stem cell2.22e-15436
stem cell7.51e-15444
motile cell3.19e-14390
mature alpha-beta T cell6.90e-0918
alpha-beta T cell6.90e-0918
immature T cell6.90e-0918
mature T cell6.90e-0918
immature alpha-beta T cell6.90e-0918
T cell6.99e-0825
pro-T cell6.99e-0825
intermediate monocyte3.70e-079
CD14-positive, CD16-positive monocyte3.70e-079
Uber Anatomy
Ontology termp-valuen
hematopoietic system5.46e-34102
blood island5.46e-34102
hemolymphoid system1.32e-28112
bone marrow1.44e-2780
bone element7.60e-2786
skeletal element2.36e-25101
skeletal system2.36e-25101
connective tissue1.73e-17375
musculoskeletal system4.81e-16167
immune system4.63e-15115
lateral plate mesoderm5.07e-08216


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
CCNT2#90536.336201576962630.003930750035764890.0189050703654271
E2F1#186934.907389214879320.008460985347239390.0323387684786948
E2F4#1874312.66806031528440.0004917987006298980.00435094997840627
E2F6#187635.017155731697390.00791769806886330.0320224787442983
EGR1#195834.988179094810140.008056488137383440.0318921868089372
ELF1#199734.258097958807540.01295179875054610.0459811309303244
ETS1#211339.728760922202340.001085840092584840.0075946995331816
FOS#235338.99795530889440.001372499272417130.00894492677141794
GABPB1#255337.067683836182170.002832212825417420.0153611069419282
HMGN3#932438.178547723350590.001827766942164210.0108257330954851
IRF1#365937.63716375356390.002244692747297240.0127562012098692
NFKB1#479035.488063424193840.006049381815655430.0268447583363177
PAX5#507936.669565531177830.003370290999677260.0172197946145146
SIN3A#2594235.408884726815140.006318961977991520.0275275744564719
TCF7L2#6934310.77017656313730.0008003181298398380.00611488954293239
THAP1#55145331.36914460285133.23800758564397e-050.00064487847871295
YY1#752834.911170749853860.008441455341808260.0327775273987104
ZBTB7A#5134137.35190930787590.002516255860282270.0139569411966658
ZNF263#1012738.221841637010680.001799043925565870.0108890378755244



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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