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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C2856_Mast_Neutrophils_Eosinophils_CD14_CD133_CD34_immature
|full_id=C2856_Mast_Neutrophils_Eosinophils_CD14_CD133_CD34_immature
|id=C2856
|id=C2856

Revision as of 15:39, 12 September 2012


Full id: C2856_Mast_Neutrophils_Eosinophils_CD14_CD133_CD34_immature



Phase1 CAGE Peaks

Hg19::chr6:31702520..31702537,-p@chr6:31702520..31702537
-
Hg19::chr6:31705781..31705817,-p@chr6:31705781..31705817
-
Hg19::chr6:31705825..31705837,-p@chr6:31705825..31705837
-
Hg19::chr6:31705970..31706014,+p@chr6:31705970..31706014
+


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 cell6.44e-53182
hematopoietic stem cell7.92e-51172
angioblastic mesenchymal cell7.92e-51172
hematopoietic oligopotent progenitor cell6.19e-47165
hematopoietic multipotent progenitor cell6.19e-47165
myeloid cell1.80e-39112
common myeloid progenitor1.80e-39112
leukocyte6.76e-39140
hematopoietic lineage restricted progenitor cell6.47e-34124
myeloid leukocyte7.95e-3176
nongranular leukocyte5.61e-30119
granulocyte monocyte progenitor cell4.52e-2771
CD14-positive, CD16-negative classical monocyte3.61e-2642
myeloid lineage restricted progenitor cell6.68e-2670
classical monocyte1.61e-2345
macrophage dendritic cell progenitor2.63e-2365
monopoietic cell2.87e-2263
monocyte2.87e-2263
monoblast2.87e-2263
promonocyte2.87e-2263
mesenchymal cell3.22e-18358
connective tissue cell9.01e-18365
motile cell8.53e-16390
multi fate stem cell3.70e-15430
stem cell4.04e-15444
somatic stem cell3.52e-14436
somatic cell4.83e-09591
lymphoid lineage restricted progenitor cell3.43e-0852
lymphocyte1.10e-0753
common lymphoid progenitor1.10e-0753
granulocyte9.27e-078
Uber Anatomy
Ontology termp-valuen
hemolymphoid system8.51e-34112
hematopoietic system7.71e-33102
blood island7.71e-33102
bone marrow3.94e-2480
bone element1.63e-2286
immune system4.12e-22115
lateral plate mesoderm4.46e-21216
skeletal element2.36e-18101
skeletal system2.36e-18101
connective tissue1.63e-17375
musculoskeletal system3.55e-09167
blood1.61e-0815
haemolymphatic fluid1.61e-0815
organism substance1.61e-0815
Disease
Ontology termp-valuen
leukemia3.19e-1139
myeloid leukemia9.38e-1131
hematologic cancer1.50e-1051
immune system cancer1.50e-1051


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-065.90511587620871e-05
E2F6#187645.017155731697390.00157802193473060.00999012140639686
ELF1#199744.258097958807540.003041525565781240.016122926026019
EP300#203346.77394172622320.0004748459821442640.00435174092042513
GTF2F1#296239.554745657568240.001820362319304780.010904320061134
HDAC2#3066413.41562023662633.0859005065161e-050.000628364911288818
HEY1#2346244.040111043105710.00375304636917980.0186560880414455
JUN#3725412.51282919233634.07770316866756e-050.000744920834760314
JUND#372746.994663941871030.000417684217818580.00392500648054298
NFKB1#479045.488063424193840.001102199566301980.00769160901409944
PAX5#507935.002174148383370.01196533174786410.0435235191702137
POU2F2#545249.106124057742520.000145395665174930.00188750501867054
SIN3A#2594245.408884726815140.001168172384885160.00797925151765996
SMARCA4#65974156.7659033078881.64738581138188e-091.44702545630708e-07
SP1#666745.69838137814090.0009482606065333980.00685650716461794
SPI1#668848.204323508522730.000220661881527680.00249845037346806
SRF#6722310.34788369662590.001439893778401260.0092422756021418
STAT2#6773348.94782838983051.42094046481278e-050.000340683198357626
TBP#690843.706770687096390.005296377814784350.0244972720371241
YY1#752844.911170749853860.00171871838055440.0107043490337361



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.