Personal tools

Coexpression cluster:C1111

From FANTOM5_SSTAR

Revision as of 16:54, 8 August 2012 by Autoedit (talk | contribs)
Jump to: navigation, search


Full id: C1111_CD8_Natural_CD14_Basophils_CD4_Peripheral_immature



Phase1 CAGE Peaks

Hg19::chr10:17069064..17069080,+p@chr10:17069064..17069080
+
Hg19::chr11:58341472..58341486,+p@chr11:58341472..58341486
+
Hg19::chr12:92271876..92271896,+p@chr12:92271876..92271896
+
Hg19::chr12:92271935..92271946,+p@chr12:92271935..92271946
+
Hg19::chr1:234747186..234747197,+p@chr1:234747186..234747197
+
Hg19::chr5:42994725..42994739,-p@chr5:42994725..42994739
-
Hg19::chr5:43042044..43042056,-p@chr5:43042044..43042056
-


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
leukocyte1.45e-48140
hematopoietic stem cell2.36e-46172
angioblastic mesenchymal cell2.36e-46172
hematopoietic cell6.11e-44182
hematopoietic oligopotent progenitor cell6.38e-43165
hematopoietic multipotent progenitor cell6.38e-43165
hematopoietic lineage restricted progenitor cell1.26e-42124
nongranular leukocyte1.84e-39119
CD14-positive, CD16-negative classical monocyte3.90e-3042
mesenchymal cell4.09e-29358
classical monocyte2.23e-2845
connective tissue cell1.43e-27365
myeloid leukocyte1.66e-2776
myeloid cell1.15e-25112
common myeloid progenitor1.15e-25112
granulocyte monocyte progenitor cell2.04e-2571
myeloid lineage restricted progenitor cell3.79e-2470
multi fate stem cell4.88e-23430
macrophage dendritic cell progenitor1.13e-2265
stem cell1.67e-22444
somatic stem cell2.75e-22436
motile cell1.73e-21390
monopoietic cell2.31e-2163
monocyte2.31e-2163
monoblast2.31e-2163
promonocyte2.31e-2163
lymphoid lineage restricted progenitor cell3.59e-1652
lymphocyte1.65e-1553
common lymphoid progenitor1.65e-1553
mature alpha-beta T cell1.64e-0918
alpha-beta T cell1.64e-0918
immature T cell1.64e-0918
mature T cell1.64e-0918
immature alpha-beta T cell1.64e-0918
T cell1.87e-0925
pro-T cell1.87e-0925
somatic cell1.70e-08591
intermediate monocyte4.02e-079
CD14-positive, CD16-positive monocyte4.02e-079
native cell4.11e-07722
Uber Anatomy
Ontology termp-valuen
connective tissue3.55e-27375
hematopoietic system7.10e-27102
blood island7.10e-27102
hemolymphoid system3.50e-25112
bone marrow1.62e-2380
bone element7.42e-2286
immune system1.66e-20115
skeletal element1.19e-17101
skeletal system1.19e-17101
lateral plate mesoderm2.72e-10216
musculoskeletal system7.69e-08167


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.