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Coexpression cluster:C3474: Difference between revisions

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|tf_chipseq_enrich=CEBPB#1051;3:7.97114762582482:0.00197418705528856:0.0115069830264137!NR3C1#2908;3:14.973023331173:0.000297833119467548:0.003083405349333!SPI1#6688;3:8.20432350852273:0.00181059318941052:0.010894540652696
|tf_chipseq_enrich=CEBPB#1051;3:7.97114762582482:0.00197418705528856:0.0115069830264137!NR3C1#2908;3:14.973023331173:0.000297833119467548:0.003083405349333!SPI1#6688;3:8.20432350852273:0.00181059318941052:0.010894540652696
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}}
}}

Revision as of 16:09, 26 November 2012


Full id: C3474_large_CD14CD16_CD14_Basophils_Peripheral_Whole_thalamus



Phase1 CAGE Peaks

Hg19::chr15:22550731..22550738,+p@chr15:22550731..22550738
+
Hg19::chr15:22550751..22550779,+p@chr15:22550751..22550779
+
Hg19::chr15:22550782..22550787,+p@chr15:22550782..22550787
+


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
classical monocyte1.04e-5642
CD14-positive, CD16-negative classical monocyte1.04e-5642
defensive cell4.59e-4948
phagocyte4.59e-4948
intermediate monocyte4.65e-419
CD14-positive, CD16-positive monocyte4.65e-419
monopoietic cell2.35e-3859
monocyte2.35e-3859
monoblast2.35e-3859
promonocyte2.35e-3859
myeloid leukocyte1.93e-3772
macrophage dendritic cell progenitor5.65e-3761
myeloid lineage restricted progenitor cell7.03e-3466
granulocyte monocyte progenitor cell2.58e-3367
nongranular leukocyte5.94e-31115
leukocyte6.00e-30136
stuff accumulating cell4.69e-2587
hematopoietic lineage restricted progenitor cell9.22e-25120
myeloid cell1.82e-23108
common myeloid progenitor1.82e-23108
hematopoietic stem cell3.37e-23168
angioblastic mesenchymal cell3.37e-23168
hematopoietic cell9.78e-22177
hematopoietic oligopotent progenitor cell1.13e-20161
hematopoietic multipotent progenitor cell1.13e-20161
non-classical monocyte3.98e-193
CD14-low, CD16-positive monocyte3.98e-193
basophil7.78e-093
single nucleate cell1.39e-083
mononuclear cell1.39e-083
mesenchymal cell5.29e-08354
connective tissue cell9.81e-08361
motile cell8.61e-07386
innate effector T cell9.73e-071
immature NK T cell9.73e-071
effector T cell9.73e-071
mature NK T cell9.73e-071
immature NK T cell stage IV9.73e-071
immature NK T cell stage I9.73e-071
immature NK T cell stage II9.73e-071
immature NK T cell stage III9.73e-071
Uber Anatomy
Ontology termp-valuen
hematopoietic system1.99e-3198
blood island1.99e-3198
bone marrow6.78e-2976
hemolymphoid system4.54e-28108
bone element1.76e-2682
immune system3.07e-2593
skeletal element9.34e-2490
skeletal system5.87e-21100
lateral plate mesoderm1.41e-12203
musculoskeletal system8.14e-11167
connective tissue2.28e-07371


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
CEBPB#105137.971147625824820.001974187055288560.0115069830264137
NR3C1#2908314.9730233311730.0002978331194675480.003083405349333
SPI1#668838.204323508522730.001810593189410520.010894540652696



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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