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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C2036_CD34_chronic_migratory_Melanocyte_Mast_acute_heart
|full_id=C2036_CD34_chronic_migratory_Melanocyte_Mast_acute_heart
|id=C2036
|id=C2036

Revision as of 14:42, 12 September 2012


Full id: C2036_CD34_chronic_migratory_Melanocyte_Mast_acute_heart



Phase1 CAGE Peaks

Hg19::chr10:11207051..11207081,+p2@CELF2
Hg19::chr10:11207088..11207095,+p17@CELF2
Hg19::chr10:11207117..11207128,+p14@CELF2
Hg19::chr10:11207157..11207175,+p13@CELF2


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 cell5.97e-46172
angioblastic mesenchymal cell5.97e-46172
hematopoietic oligopotent progenitor cell1.67e-42165
hematopoietic multipotent progenitor cell1.67e-42165
hematopoietic cell6.86e-42182
leukocyte1.72e-32140
myeloid cell6.30e-29112
common myeloid progenitor6.30e-29112
hematopoietic lineage restricted progenitor cell2.45e-24124
nongranular leukocyte3.75e-23119
myeloid leukocyte1.50e-1576
T cell1.23e-1325
pro-T cell1.23e-1325
granulocyte monocyte progenitor cell1.32e-1371
mesenchymal cell9.68e-13358
myeloid lineage restricted progenitor cell3.74e-1270
motile cell3.88e-12390
lymphoid lineage restricted progenitor cell5.22e-1252
lymphocyte5.63e-1253
common lymphoid progenitor5.63e-1253
connective tissue cell1.70e-11365
CD14-positive, CD16-negative classical monocyte4.22e-1142
mature alpha-beta T cell8.64e-1118
alpha-beta T cell8.64e-1118
immature T cell8.64e-1118
mature T cell8.64e-1118
immature alpha-beta T cell8.64e-1118
macrophage dendritic cell progenitor1.16e-1065
monopoietic cell3.08e-1063
monocyte3.08e-1063
monoblast3.08e-1063
promonocyte3.08e-1063
classical monocyte6.56e-0945
stem cell1.03e-08444
multi fate stem cell1.53e-08430
somatic stem cell1.48e-07436
Uber Anatomy
Ontology termp-valuen
adult organism4.55e-21115
hematopoietic system1.60e-18102
blood island1.60e-18102
hemolymphoid system8.33e-15112
neural tube3.41e-1257
neural rod3.41e-1257
future spinal cord3.41e-1257
neural keel3.41e-1257
bone marrow5.14e-1280
anterior neural tube6.29e-1142
regional part of forebrain1.33e-1041
forebrain1.33e-1041
future forebrain1.33e-1041
gray matter2.46e-1034
brain grey matter2.46e-1034
connective tissue2.79e-10375
telencephalon3.84e-1034
regional part of telencephalon4.65e-1033
cerebral hemisphere5.94e-1032
bone element8.19e-1086
regional part of brain4.25e-0959
central nervous system5.89e-0982
cerebral cortex1.32e-0725
pallium1.32e-0725
skeletal element2.66e-07101
skeletal system2.66e-07101
regional part of cerebral cortex2.79e-0722
regional part of nervous system2.79e-0794
nervous system2.79e-0794
neural plate3.65e-0786
presumptive neural plate3.65e-0786
neocortex6.66e-0720
Disease
Ontology termp-valuen
leukemia1.37e-1539
myeloid leukemia1.94e-1331
hematologic cancer5.88e-1351
immune system cancer5.88e-1351


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#187645.017155731697390.00157802193473060.0099467096892588
FOS#235348.99795530889440.0001525147711168630.00194510809386666
FOSL1#8061439.7135797163734.01511434669553e-071.93509241926412e-05
HEY1#2346244.040111043105710.00375304636917980.0185439944055812
MAX#414946.452555509007120.0005767613195645490.00484254163952102
NRF1#4899412.21027944771094.49717228915276e-050.00079150687008228
PAX5#507946.669565531177830.0005052774169483260.00442892724705549
POU2F2#545249.106124057742520.000145395665174930.00187956156395649
SIN3A#2594245.408884726815140.001168172384885160.00793823643080362
TAF1#687243.343046285745290.008005664898701650.0321035031621679
TAL1#6886429.86861667744021.25525650806991e-065.02868179694335e-05
TBP#690843.706770687096390.005296377814784350.0243366801266339
YY1#752844.911170749853860.00171871838055440.0106585849383481
ZNF263#1012748.221841637010680.0002187871180958320.00247964273758118



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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