Personal tools

Coexpression cluster:C3269

From FANTOM5_SSTAR

Revision as of 05:34, 21 May 2012 by Autoedit (talk | contribs)
Jump to: navigation, search


Full id: C3269_Hodgkin_thymus_acute_Burkitt_mycosis_non_B



Phase1 CAGE Peaks

  Short description
Hg19::chr12:25205155..25205214,+ p3@LRMP
Hg19::chr12:25205221..25205232,+ p11@LRMP
Hg19::chr12:25205248..25205262,+ p8@LRMP


Enriched pathways on this co-expression clusterSummary:
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.
Analyst: Emmanuel Dimont

link to source dataset
data


No results for this coexpression

Enriched Gene Ontology terms on this co-expression clusterSummary: 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.
Analyst: Erik Arner

link to source dataset
data


No GOStat results

Enriched sample ontology terms on this co-expression clusterSummary: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. Analyst: Hideya Kawaji

links to source dataset

cell_data
uberon_data
disease_data


Cell Type
Ontology termp-valuen
hematopoietic stem cell2.87e-66172
angioblastic mesenchymal cell2.87e-66172
hematopoietic cell2.79e-63182
hematopoietic oligopotent progenitor cell5.56e-61165
hematopoietic multipotent progenitor cell5.56e-61165
leukocyte3.28e-58140
hematopoietic lineage restricted progenitor cell3.40e-47124
nongranular leukocyte8.22e-46119
lymphocyte2.77e-3353
common lymphoid progenitor2.77e-3353
lymphoid lineage restricted progenitor cell1.07e-3252
myeloid cell4.05e-27112
common myeloid progenitor4.05e-27112
myeloid leukocyte7.42e-2076
T cell2.01e-1825
pro-T cell2.01e-1825
myeloid lineage restricted progenitor cell3.48e-1670
granulocyte monocyte progenitor cell8.90e-1671
CD14-positive, CD16-negative classical monocyte8.25e-1542
mature alpha-beta T cell2.35e-1418
alpha-beta T cell2.35e-1418
immature T cell2.35e-1418
mature T cell2.35e-1418
immature alpha-beta T cell2.35e-1418
lymphocyte of B lineage5.27e-1324
pro-B cell5.27e-1324
macrophage dendritic cell progenitor5.98e-1365
monopoietic cell6.65e-1363
monocyte6.65e-1363
monoblast6.65e-1363
promonocyte6.65e-1363
classical monocyte6.91e-1345
CD8-positive, alpha-beta T cell2.33e-0911
mesenchymal cell1.04e-07358
connective tissue cell7.19e-07365
Uber Anatomy
Ontology termp-valuen
hematopoietic system4.38e-25102
blood island4.38e-25102
hemolymphoid system2.47e-24112
adult organism9.87e-23115
bone marrow1.93e-1380
immune system3.18e-11115
bone element3.37e-1186
blood2.18e-1015
haemolymphatic fluid2.18e-1015
organism substance2.18e-1015
skeletal element6.88e-08101
skeletal system6.88e-08101
Disease
Ontology termp-valuen
hematologic cancer7.77e-1651
immune system cancer7.77e-1651
leukemia3.65e-1139
lymphoma3.03e-0810
myeloid leukemia6.62e-0731


Overrepresented TFBS (DNA) motifs on this co-expression clusterSummary: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. Analyst: Michiel de Hoon

link to source data
Novel motifs
data

Jaspar motifs
data


Novel motifs



JASPAR motifs

Motifs-log10(p-value)

{{{tfbs_overrepresentation_jaspar}}}



ENCODE TF ChIP-seq peak enrichment analysisSummary: 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.
Analyst: Erik Arner

link to source dataset

data


No analysis results for this cluster

Relative expression of the co-expression clusterSummary:Co-expression clusters are compared against FANTOM5 samples to obtain relative expression.
Analyst:NA

link to data source
data


This analysis result is provided for C0 - C305 clusters.