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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C451_CD14_CD4_Eosinophils_Neutrophils_adult_Natural_CD8
|full_id=C451_CD14_CD4_Eosinophils_Neutrophils_adult_Natural_CD8
|id=C451
|id=C451

Revision as of 17:36, 12 September 2012


Full id: C451_CD14_CD4_Eosinophils_Neutrophils_adult_Natural_CD8



Phase1 CAGE Peaks

Hg19::chr12:48592134..48592150,+p1@DKFZP779L1853
Hg19::chr12:66696322..66696383,+p2@HELB
Hg19::chr16:50715196..50715235,-p1@SNX20
Hg19::chr16:57023445..57023514,+p1@NLRC5
Hg19::chr16:57025612..57025617,+p@chr16:57025612..57025617
+
Hg19::chr16:89787973..89788001,+p3@ZNF276
Hg19::chr16:89788512..89788554,-p@chr16:89788512..89788554
-
Hg19::chr17:33701610..33701646,-p@chr17:33701610..33701646
-
Hg19::chr17:78237438..78237452,+p1@CU691854
Hg19::chr19:1133589..1133603,-p@chr19:1133589..1133603
-
Hg19::chr1:89664595..89664636,-p1@GBP4
Hg19::chr1:89738560..89738575,-p2@GBP5
Hg19::chr22:36556793..36556811,-p1@APOL3
Hg19::chr2:240189135..240189153,-p@chr2:240189135..240189153
-
Hg19::chr2:240189159..240189181,-p@chr2:240189159..240189181
-
Hg19::chr2:240189199..240189221,-p@chr2:240189199..240189221
-
Hg19::chr3:142166796..142166841,-p3@XRN1
Hg19::chr3:156893074..156893141,+p1@ENST00000488040
Hg19::chr5:42992974..42992986,-p6@uc003jnb.1
Hg19::chr6:106545946..106545979,+p@chr6:106545946..106545979
+
Hg19::chr6:18265050..18265072,-p5@DEK
Hg19::chr6:32811888..32811906,+p1@ENST00000413039
p1@ENST00000429600
p1@ENST00000458296


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
hematopoietic stem cell3.66e-59172
angioblastic mesenchymal cell3.66e-59172
leukocyte2.08e-57140
hematopoietic cell1.03e-55182
hematopoietic oligopotent progenitor cell1.37e-55165
hematopoietic multipotent progenitor cell1.37e-55165
nongranular leukocyte2.89e-49119
hematopoietic lineage restricted progenitor cell4.06e-49124
myeloid cell1.70e-30112
common myeloid progenitor1.70e-30112
myeloid leukocyte2.46e-2976
granulocyte monocyte progenitor cell2.57e-2571
myeloid lineage restricted progenitor cell7.47e-2570
macrophage dendritic cell progenitor8.55e-2465
monopoietic cell1.26e-2363
monocyte1.26e-2363
monoblast1.26e-2363
promonocyte1.26e-2363
CD14-positive, CD16-negative classical monocyte3.99e-2342
lymphoid lineage restricted progenitor cell1.04e-2252
lymphocyte1.31e-2253
common lymphoid progenitor1.31e-2253
classical monocyte4.93e-2145
mesenchymal cell1.24e-14358
T cell1.91e-1325
pro-T cell1.91e-1325
connective tissue cell4.69e-13365
mature alpha-beta T cell3.53e-1218
alpha-beta T cell3.53e-1218
immature T cell3.53e-1218
mature T cell3.53e-1218
immature alpha-beta T cell3.53e-1218
motile cell7.45e-09390
lymphocyte of B lineage8.26e-0924
pro-B cell8.26e-0924
CD8-positive, alpha-beta T cell2.99e-0811
Uber Anatomy
Ontology termp-valuen
hemolymphoid system1.69e-33112
hematopoietic system1.12e-32102
blood island1.12e-32102
bone marrow6.69e-2280
immune system9.12e-22115
bone element1.81e-1886
adult organism8.46e-16115
skeletal element1.10e-13101
skeletal system1.10e-13101
connective tissue3.47e-12375
blood5.82e-0915
haemolymphatic fluid5.82e-0915
organism substance5.82e-0915
lateral plate mesoderm1.82e-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
BCL11A#5333556.447603432637970.0008654585595952050.00645902719062195
EBF1#1879104.048394021167735.69071288955694e-050.000949564408807217
ELF1#1997152.903248608277871.09648915323577e-050.000284088887806476
GATA1#262374.314643500300140.0007492385419969230.00589896148417766
IRF4#366254.980571065169120.002710389575557860.0148890372860134
MEF2A#420554.259825206737280.005297580344031970.0243400639457285
NFKB1#4790112.744031712096920.000705788843196090.00567319949161521
PAX5#5079103.031620695989920.0006486935838301440.0053148904998538
POLR2A#5430212.04984166853271.30673372631837e-065.18518098947434e-05
PRDM1#639317.97694851510830.0006021829833485840.00503090861514621
SMC3#912653.419302919302920.01314679266670590.0466163468227777
SPI1#668872.610466570893590.01288045219699750.0463326288834546
STAT1#677287.52966818079975.11850336669685e-060.000157273131248736
STAT2#6773514.83267526964561.78325817125753e-050.000406907800192191
STAT3#677494.303417498835839.9173625749362e-050.00139609034905481



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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