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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C2741_B_CD14_splenic_immature_b_Mast_xeroderma
|full_id=C2741_B_CD14_splenic_immature_b_Mast_xeroderma
|id=C2741
|id=C2741

Revision as of 15:31, 12 September 2012


Full id: C2741_B_CD14_splenic_immature_b_Mast_xeroderma



Phase1 CAGE Peaks

Hg19::chr3:47032417..47032436,+p@chr3:47032417..47032436
+
Hg19::chr7:20259717..20259736,-p@chr7:20259717..20259736
-
Hg19::chr9:128394685..128394703,-p@chr9:128394685..128394703
-
Hg19::chrX:13024034..13024045,+p@chrX:13024034..13024045
+


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
leukocyte2.02e-60140
CD14-positive, CD16-negative classical monocyte6.80e-6042
classical monocyte4.04e-5545
nongranular leukocyte8.69e-52119
hematopoietic lineage restricted progenitor cell2.79e-51124
myeloid leukocyte9.81e-4876
granulocyte monocyte progenitor cell2.97e-4771
hematopoietic cell5.80e-47182
hematopoietic stem cell1.27e-45172
angioblastic mesenchymal cell1.27e-45172
myeloid lineage restricted progenitor cell1.80e-4570
macrophage dendritic cell progenitor4.98e-4565
hematopoietic oligopotent progenitor cell5.79e-45165
hematopoietic multipotent progenitor cell5.79e-45165
monopoietic cell4.13e-4463
monocyte4.13e-4463
monoblast4.13e-4463
promonocyte4.13e-4463
myeloid cell1.20e-34112
common myeloid progenitor1.20e-34112
lymphocyte of B lineage1.19e-1624
pro-B cell1.19e-1624
mesenchymal cell6.59e-13358
connective tissue cell2.57e-12365
motile cell2.97e-10390
lymphocyte2.01e-0953
common lymphoid progenitor2.01e-0953
circulating cell6.04e-096
lymphoid lineage restricted progenitor cell1.30e-0852
intermediate monocyte2.06e-089
CD14-positive, CD16-positive monocyte2.06e-089
multi fate stem cell7.68e-08430
conventional dendritic cell9.20e-088
stem cell1.48e-07444
somatic stem cell1.67e-07436
Langerhans cell3.60e-075
Uber Anatomy
Ontology termp-valuen
hematopoietic system4.39e-49102
blood island4.39e-49102
bone marrow1.33e-4480
hemolymphoid system2.65e-43112
bone element1.47e-4086
skeletal element3.75e-34101
skeletal system3.75e-34101
immune system6.60e-33115
lateral plate mesoderm7.80e-17216
musculoskeletal system1.92e-16167
connective tissue1.63e-11375


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
BATF#10538318.26835134422770.0002681660105721290.00286780565002484
BCL11A#53335428.36945510360711.542446414682e-065.89862911398658e-05
BCLAF1#9774210.82632380506090.01202203816432580.043662875359717
CHD2#110637.758017125587640.003351522464536340.0173059257724568
EBF1#187948.9064668465690.00015887907472010.00199917731140874
EP300#203346.77394172622320.0004748459821442640.00434830684166285
HNF4A#3172211.56614518147680.01057585681762490.0390763429624259
HNF4G#3174214.37671126322340.006924169980439180.0293095038538924
IRF4#3662316.43588451505810.0003669431395554610.003659585041256
MEF2A#4205418.74323090964418.0978922767748e-060.000224571367895402
MEF2C#4208330.9835158694685.56692972943475e-050.00094185092177618
NFKB1#479045.488063424193840.001102199566301980.0076885266166853
PAX5#507946.669565531177830.0005052774169483260.00444571761993818
PBX3#5090210.95725634337210.01174530180688030.0428590047660381
POU2F2#545249.106124057742520.000145395665174930.00188539581266507
SP1#666745.69838137814090.0009482606065333980.00685223756214914
SPI1#668848.204323508522730.000220661881527680.00249709678674498
TCF12#693837.975848676639820.003090920396013070.0162863949971853



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.