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Coexpression cluster:C2141: Difference between revisions

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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C2141_Neutrophils_Macrophage_CD14_Monocytederived_Eosinophils_Dendritic_CD14CD16
|full_id=C2141_Neutrophils_Macrophage_CD14_Monocytederived_Eosinophils_Dendritic_CD14CD16
|gostat_on_coexpression_clusters=GO:0015198!oligopeptide transporter activity!0.0376664433950366!51296$GO:0015197!peptide transporter activity!0.0376664433950366!51296$GO:0015026!coreceptor activity!0.0400046939624358!23643$GO:0006857!oligopeptide transport!0.0400046939624358!51296
|gostat_on_coexpression_clusters=GO:0015198!oligopeptide transporter activity!0.0376664433950366!51296$GO:0015197!peptide transporter activity!0.0376664433950366!51296$GO:0015026!coreceptor activity!0.0400046939624358!23643$GO:0006857!oligopeptide transport!0.0400046939624358!51296

Revision as of 14:49, 12 September 2012


Full id: C2141_Neutrophils_Macrophage_CD14_Monocytederived_Eosinophils_Dendritic_CD14CD16



Phase1 CAGE Peaks

Hg19::chr11:60719607..60719659,-p1@SLC15A3
Hg19::chr14:93118813..93118870,+p5@RIN3
Hg19::chr5:179498703..179498784,-p1@RNF130
Hg19::chr8:74903580..74903661,+p1@LY96


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


GO IDGO nameFDR corrected p-value
GO:0015198oligopeptide transporter activity0.0376664433950366
GO:0015197peptide transporter activity0.0376664433950366
GO:0015026coreceptor activity0.0400046939624358
GO:0006857oligopeptide transport0.0400046939624358



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
myeloid leukocyte1.46e-3476
granulocyte monocyte progenitor cell4.51e-2971
monopoietic cell3.14e-2763
monocyte3.14e-2763
monoblast3.14e-2763
promonocyte3.14e-2763
myeloid lineage restricted progenitor cell6.45e-2770
macrophage dendritic cell progenitor6.69e-2765
CD14-positive, CD16-negative classical monocyte2.81e-2542
leukocyte3.91e-25140
myeloid cell1.80e-24112
common myeloid progenitor1.80e-24112
classical monocyte1.03e-2045
hematopoietic stem cell5.43e-20172
angioblastic mesenchymal cell5.43e-20172
hematopoietic oligopotent progenitor cell2.33e-18165
hematopoietic multipotent progenitor cell2.33e-18165
nongranular leukocyte6.29e-18119
hematopoietic cell2.82e-17182
hematopoietic lineage restricted progenitor cell5.61e-17124
mesenchymal cell3.41e-11358
connective tissue cell1.39e-10365
multi fate stem cell1.81e-09430
motile cell1.99e-08390
stem cell2.36e-08444
somatic stem cell2.88e-08436
Uber Anatomy
Ontology termp-valuen
hemolymphoid system8.33e-33112
hematopoietic system2.19e-31102
blood island2.19e-31102
adult organism3.02e-29115
bone marrow1.77e-2780
immune system1.55e-25115
bone element7.22e-2486
skeletal element2.02e-19101
skeletal system2.02e-19101
lateral plate mesoderm1.67e-16216
musculoskeletal system2.76e-13167
connective tissue7.12e-10375
neural tube4.28e-0757
neural rod4.28e-0757
future spinal cord4.28e-0757
neural keel4.28e-0757


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#668848.204323508522730.000220661881527680.00249035079369671



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.