Personal tools

Coexpression cluster:C4278

From FANTOM5_SSTAR

Revision as of 15:49, 19 October 2012 by Autoedit (talk | contribs)
Jump to: navigation, search


Full id: C4278_liver_Monocytederived_hepatocellular_Macrophage_Hepatocyte_CD14_small



Phase1 CAGE Peaks

Hg19::chr3:126242976..126243008,+p1@CHST13
Hg19::chr3:126243130..126243153,+p2@CHST13
Hg19::chr3:126243162..126243176,+p3@CHST13


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
myeloid leukocyte5.17e-4672
granulocyte monocyte progenitor cell3.72e-4167
myeloid lineage restricted progenitor cell3.75e-4066
monopoietic cell2.32e-3959
monocyte2.32e-3959
monoblast2.32e-3959
promonocyte2.32e-3959
macrophage dendritic cell progenitor2.04e-3761
myeloid cell3.21e-35108
common myeloid progenitor3.21e-35108
defensive cell1.49e-3348
phagocyte1.49e-3348
classical monocyte6.70e-2742
CD14-positive, CD16-negative classical monocyte6.70e-2742
hematopoietic stem cell1.91e-19168
angioblastic mesenchymal cell1.91e-19168
hematopoietic cell2.78e-19177
leukocyte4.73e-19136
hematopoietic oligopotent progenitor cell4.57e-18161
hematopoietic multipotent progenitor cell4.57e-18161
nongranular leukocyte2.86e-16115
hematopoietic lineage restricted progenitor cell6.84e-16120
stuff accumulating cell1.23e-1387
intermediate monocyte2.11e-099
CD14-positive, CD16-positive monocyte2.11e-099
macrophage1.86e-086
Uber Anatomy
Ontology termp-valuen
hematopoietic system9.03e-4798
blood island9.03e-4798
hemolymphoid system7.49e-41108
bone marrow1.71e-3576
bone element8.74e-3582
skeletal element1.07e-2990
immune system3.21e-2993
skeletal system1.52e-24100
blood1.36e-1315
haemolymphatic fluid1.36e-1315
organism substance1.36e-1315
lateral plate mesoderm3.98e-11203
musculoskeletal system1.92e-08167
larynx2.37e-079


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
CTCF#1066435.360256373075030.0064925092527670.0280391669292368
E2F1#186934.907389214879320.008460985347239390.0326518437970785
GABPB1#255337.067683836182170.002832212825417420.0154525898690717
HNF4A#3172323.13229036295378.07584663437677e-050.00123110983308667
HNF4G#3174328.75342252644684.20470658818262e-050.0007586996395356
SP1#666735.69838137814090.005403962701712170.0247211765485816



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.