Personal tools

Coexpression cluster:C2052

From FANTOM5_SSTAR

Revision as of 12:00, 19 October 2012 by Autoedit (talk | contribs)
Jump to: navigation, search


Full id: C2052_CD133_CD34_CD14_Basophils_chronic_Peripheral_leukemia



Phase1 CAGE Peaks

Hg19::chr10:27742148..27742150,+p@chr10:27742148..27742150
+
Hg19::chr13:32483542..32483546,+p@chr13:32483542..32483546
+
Hg19::chr3:14733266..14733274,+p@chr3:14733266..14733274
+
Hg19::chr4:55234775..55234779,-p@chr4:55234775..55234779
-


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
classical monocyte3.85e-6942
CD14-positive, CD16-negative classical monocyte3.85e-6942
myeloid cell1.88e-65108
common myeloid progenitor1.88e-65108
granulocyte monocyte progenitor cell7.89e-6467
macrophage dendritic cell progenitor2.62e-6061
defensive cell2.24e-5948
phagocyte2.24e-5948
myeloid leukocyte5.56e-5972
myeloid lineage restricted progenitor cell4.96e-5866
monopoietic cell1.57e-5559
monocyte1.57e-5559
monoblast1.57e-5559
promonocyte1.57e-5559
hematopoietic stem cell2.03e-51168
angioblastic mesenchymal cell2.03e-51168
hematopoietic cell3.82e-48177
hematopoietic oligopotent progenitor cell1.61e-47161
hematopoietic multipotent progenitor cell1.61e-47161
leukocyte4.99e-43136
hematopoietic lineage restricted progenitor cell7.41e-39120
nongranular leukocyte5.19e-35115
stuff accumulating cell8.48e-2987
intermediate monocyte1.09e-219
CD14-positive, CD16-positive monocyte1.09e-219
mesenchymal cell1.91e-17354
connective tissue cell7.56e-17361
motile cell9.61e-15386
multi fate stem cell6.60e-13427
stem cell6.71e-13441
somatic stem cell1.53e-12433
CD1a-positive Langerhans cell3.74e-072
immature CD1a-positive Langerhans cell3.74e-072
Uber Anatomy
Ontology termp-valuen
bone marrow1.82e-5876
bone element1.88e-5382
hematopoietic system3.68e-4898
blood island3.68e-4898
skeletal element8.45e-4890
immune system6.28e-4693
hemolymphoid system1.03e-42108
skeletal system5.39e-42100
musculoskeletal system5.34e-21167
lateral plate mesoderm1.07e-17203
connective tissue4.94e-16371
mesoderm2.32e-08315
mesoderm-derived structure2.32e-08315
presumptive mesoderm2.32e-08315
Disease
Ontology termp-valuen
myeloid leukemia2.14e-0931
leukemia5.11e-0739
hematologic cancer5.82e-0751
immune system cancer5.82e-0751


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


No analysis results for this cluster

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.