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Coexpression cluster:C1939


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Full id: C1939_cord_myeloma_CD14_Neutrophils_b_Whole_anaplastic

Phase1 CAGE Peaks


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 monocyte8.76e-9142
CD14-positive, CD16-negative classical monocyte8.76e-9142
defensive cell1.29e-8348
monopoietic cell2.65e-6559
myeloid leukocyte5.01e-6372
macrophage dendritic cell progenitor6.10e-6361
myeloid lineage restricted progenitor cell1.19e-5766
granulocyte monocyte progenitor cell1.10e-5667
nongranular leukocyte1.21e-54115
hematopoietic lineage restricted progenitor cell7.71e-47120
hematopoietic cell9.57e-45177
stuff accumulating cell1.44e-4287
hematopoietic stem cell1.27e-40168
angioblastic mesenchymal cell1.27e-40168
myeloid cell2.01e-39108
common myeloid progenitor2.01e-39108
hematopoietic oligopotent progenitor cell1.20e-38161
hematopoietic multipotent progenitor cell1.20e-38161
circulating cell4.68e-176
mesenchymal cell2.92e-14354
connective tissue cell8.53e-14361
motile cell3.71e-12386
multi fate stem cell3.75e-10427
somatic stem cell7.08e-10433
stem cell1.61e-09441
intermediate monocyte4.91e-079
CD14-positive, CD16-positive monocyte4.91e-079
Uber Anatomy
Ontology termp-valuen
hematopoietic system1.20e-5998
blood island1.20e-5998
hemolymphoid system2.43e-53108
bone marrow1.19e-5276
bone element2.94e-4882
immune system2.66e-4493
skeletal element2.67e-4390
skeletal system3.30e-38100
lateral plate mesoderm3.06e-24203
musculoskeletal system9.56e-20167
connective tissue3.68e-13371
mesoderm-derived structure2.10e-12315
presumptive mesoderm2.10e-12315
haemolymphatic fluid2.94e-0915
organism substance2.94e-0915

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



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)


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.