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Coexpression cluster:C2288

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Full id: C2288_mesothelioma_colon_small_Intestinal_Prostate_CD14_Macrophage



Phase1 CAGE Peaks

Hg19::chr14:23284561..23284595,-p2@SLC7A7
Hg19::chr14:23284599..23284616,-p4@SLC7A7
Hg19::chr14:23284630..23284650,-p1@SLC7A7
Hg19::chr14:23284675..23284684,-p11@SLC7A7


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
monopoietic cell5.69e-3859
monocyte5.69e-3859
monoblast5.69e-3859
promonocyte5.69e-3859
macrophage dendritic cell progenitor1.23e-3561
defensive cell2.72e-3448
phagocyte2.72e-3448
myeloid leukocyte2.02e-3372
myeloid lineage restricted progenitor cell1.78e-3066
granulocyte monocyte progenitor cell1.51e-2967
classical monocyte2.16e-2942
CD14-positive, CD16-negative classical monocyte2.16e-2942
nongranular leukocyte8.52e-19115
leukocyte1.57e-16136
myeloid cell5.76e-15108
common myeloid progenitor5.76e-15108
stuff accumulating cell1.66e-1487
hematopoietic lineage restricted progenitor cell3.79e-14120
hematopoietic stem cell2.15e-09168
angioblastic mesenchymal cell2.15e-09168
hematopoietic cell6.46e-09177
hematopoietic oligopotent progenitor cell2.21e-08161
hematopoietic multipotent progenitor cell2.21e-08161
intermediate monocyte5.56e-089
CD14-positive, CD16-positive monocyte5.56e-089
Uber Anatomy
Ontology termp-valuen
hematopoietic system3.05e-2798
blood island3.05e-2798
hemolymphoid system5.37e-24108
bone marrow9.76e-2476
lateral plate mesoderm3.68e-23203
immune system5.92e-2093
bone element7.88e-2082
mesoderm1.89e-19315
mesoderm-derived structure1.89e-19315
presumptive mesoderm1.89e-19315
skeletal element1.37e-1590
musculoskeletal system3.28e-12167
skeletal system7.44e-12100
embryo2.55e-08592
germ layer2.85e-08560
germ layer / neural crest2.85e-08560
embryonic tissue2.85e-08560
presumptive structure2.85e-08560
germ layer / neural crest derived structure2.85e-08560
epiblast (generic)2.85e-08560
developing anatomical structure3.18e-08581
adult organism9.05e-08114
embryonic structure1.01e-07564
organ3.19e-07503
tissue7.36e-07773


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
BCLAF1#9774210.82632380506090.01202203816432580.0436492141089526
CEBPB#105147.971147625824820.0002476385788090830.0026770650587146
HNF4A#3172423.13229036295373.48990320893214e-060.000115378917770707
HNF4G#3174428.75342252644681.46167379934821e-065.65810785508258e-05
MAFK#7975427.10073313782991.85228494563408e-066.84539233676851e-05



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.