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Coexpression cluster:C3892: Difference between revisions

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|tf_chipseq_enrich=SPI1#6688;3:8.20432350852273:0.00181059318941052:0.010909625691389
|tf_chipseq_enrich=SPI1#6688;3:8.20432350852273:0.00181059318941052:0.010909625691389
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}}
}}

Revision as of 16:25, 26 November 2012


Full id: C3892_Mast_Macrophage_Monocytederived_CD14_Dendritic_acute_chronic



Phase1 CAGE Peaks

Hg19::chr1:160549235..160549303,-p1@CD84
Hg19::chr7:137620650..137620677,-p3@CREB3L2
Hg19::chr7:137620684..137620711,-p4@CREB3L2


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 cell8.25e-76168
angioblastic mesenchymal cell8.25e-76168
hematopoietic oligopotent progenitor cell1.73e-73161
hematopoietic multipotent progenitor cell1.73e-73161
hematopoietic cell4.10e-70177
myeloid cell2.21e-58108
common myeloid progenitor2.21e-58108
leukocyte5.21e-56136
hematopoietic lineage restricted progenitor cell6.24e-49120
nongranular leukocyte3.53e-47115
myeloid leukocyte2.11e-4172
myeloid lineage restricted progenitor cell8.61e-3766
granulocyte monocyte progenitor cell1.76e-3667
monopoietic cell9.06e-3359
monocyte9.06e-3359
monoblast9.06e-3359
promonocyte9.06e-3359
macrophage dendritic cell progenitor5.95e-3261
defensive cell1.77e-2848
phagocyte1.77e-2848
classical monocyte1.71e-2342
CD14-positive, CD16-negative classical monocyte1.71e-2342
nucleate cell1.14e-1355
lymphocyte2.13e-1353
common lymphoid progenitor2.13e-1353
lymphoid lineage restricted progenitor cell3.01e-1352
mature alpha-beta T cell2.33e-1118
alpha-beta T cell2.33e-1118
immature T cell2.33e-1118
mature T cell2.33e-1118
immature alpha-beta T cell2.33e-1118
mesenchymal cell1.42e-10354
stuff accumulating cell9.46e-1087
connective tissue cell1.69e-09361
T cell1.16e-0825
pro-T cell1.16e-0825
CD8-positive, alpha-beta T cell1.22e-0711
motile cell5.23e-07386
Uber Anatomy
Ontology termp-valuen
hematopoietic system2.91e-4198
blood island2.91e-4198
hemolymphoid system4.86e-36108
bone marrow1.87e-3276
immune system4.76e-3093
bone element8.23e-2882
adult organism1.18e-25114
skeletal element1.07e-2290
skeletal system7.41e-19100
neural tube2.92e-0956
neural rod2.92e-0956
future spinal cord2.92e-0956
neural keel2.92e-0956
lateral plate mesoderm9.36e-09203
connective tissue1.80e-08371
regional part of nervous system2.53e-0853
regional part of brain2.53e-0853
regional part of forebrain7.38e-0841
forebrain7.38e-0841
anterior neural tube7.38e-0841
future forebrain7.38e-0841
telencephalon7.82e-0734
Disease
Ontology termp-valuen
myeloid leukemia8.53e-1831
leukemia1.97e-1539
hematologic cancer5.28e-1251
immune system cancer5.28e-1251


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
SPI1#668838.204323508522730.001810593189410520.010909625691389



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.