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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C1261_Dendritic_CD19_CD4_CD8_CD14_Natural_Peripheral
|full_id=C1261_Dendritic_CD19_CD4_CD8_CD14_Natural_Peripheral
|id=C1261
|id=C1261

Revision as of 13:46, 12 September 2012


Full id: C1261_Dendritic_CD19_CD4_CD8_CD14_Natural_Peripheral



Phase1 CAGE Peaks

Hg19::chr21:45563531..45563542,+p@chr21:45563531..45563542
+
Hg19::chr21:45564916..45564931,-p@chr21:45564916..45564931
-
Hg19::chr3:107843890..107843896,+p@chr3:107843890..107843896
+
Hg19::chr3:88198926..88198939,+p8@C3orf38
Hg19::chr4:140005443..140005527,-p2@ELF2
Hg19::chr4:89205350..89205385,-p4@PPM1K
Hg19::chr4:89205847..89205873,-p2@PPM1K


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 cell2.49e-58172
angioblastic mesenchymal cell2.49e-58172
hematopoietic oligopotent progenitor cell1.29e-53165
hematopoietic multipotent progenitor cell1.29e-53165
hematopoietic cell1.38e-53182
leukocyte4.46e-48140
hematopoietic lineage restricted progenitor cell2.60e-39124
nongranular leukocyte4.29e-39119
lymphocyte5.26e-3053
common lymphoid progenitor5.26e-3053
lymphoid lineage restricted progenitor cell1.58e-2952
myeloid cell1.45e-23112
common myeloid progenitor1.45e-23112
lymphocyte of B lineage9.38e-1524
pro-B cell9.38e-1524
myeloid leukocyte2.27e-1476
T cell5.58e-1425
pro-T cell5.58e-1425
CD14-positive, CD16-negative classical monocyte4.14e-1342
granulocyte monocyte progenitor cell1.53e-1271
mature alpha-beta T cell5.04e-1218
alpha-beta T cell5.04e-1218
immature T cell5.04e-1218
mature T cell5.04e-1218
immature alpha-beta T cell5.04e-1218
myeloid lineage restricted progenitor cell7.22e-1270
classical monocyte1.53e-1145
macrophage dendritic cell progenitor6.12e-1165
monopoietic cell2.34e-1063
monocyte2.34e-1063
monoblast2.34e-1063
promonocyte2.34e-1063
B cell2.85e-1014
CD8-positive, alpha-beta T cell6.72e-0811
mesenchymal cell1.23e-07358
Uber Anatomy
Ontology termp-valuen
hematopoietic system4.26e-19102
blood island4.26e-19102
hemolymphoid system1.55e-17112
adult organism3.34e-14115
bone marrow3.25e-1080
bone element1.18e-0986
blood9.50e-0915
haemolymphatic fluid9.50e-0915
organism substance9.50e-0915
immune system2.33e-07115
skeletal element6.55e-07101
skeletal system6.55e-07101
Disease
Ontology termp-valuen
hematologic cancer1.66e-1351
immune system cancer1.66e-1351
leukemia1.16e-1039
myeloid leukemia1.60e-0731


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
CHD2#110657.38858773865490.0001498689600820670.00193260455883578
ELF1#199753.041498542005380.009719562269370750.0365696867155707
IRF3#3661213.42341491756850.00885816023056540.0336181327926167
MEF2C#4208211.80324414074970.01134538181234960.0416017249877109
NFKB1#479064.704054363594720.000216115061401970.00247813360757141
PAX5#507965.716770455295286.92762487228137e-050.00109939859297401
PBX3#5090412.52257867813950.0001356731131035550.00177697068716105
POLR2A#543072.147453176558070.004747636447610280.0223531874020363
TAF1#687262.865468244924540.003728330207471460.0185871916816131
TBP#690863.177232017511190.002074112051852660.0120216542862223
TCF12#693846.076837086963670.002165496819676230.01249653676374
YY1#752853.507979107038470.005072570672808980.0236158431104844



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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