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Coexpression cluster:C3497

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Full id: C3497_skeletal_CD14_Dendritic_Monocytederived_Basophils_Macrophage_immature



Phase1 CAGE Peaks

Hg19::chr15:51058130..51058152,-p2@SPPL2A
Hg19::chr8:74888516..74888527,+p3@TMEM70
Hg19::chr8:74888542..74888594,+p2@TMEM70


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


GO IDGO nameFDR corrected p-value
GO:0004190aspartic-type endopeptidase activity0.0449814078230606



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
granulocyte monocyte progenitor cell5.74e-3267
myeloid leukocyte5.54e-3172
macrophage dendritic cell progenitor2.42e-2961
myeloid lineage restricted progenitor cell6.63e-2966
monopoietic cell4.46e-2859
monocyte4.46e-2859
monoblast4.46e-2859
promonocyte4.46e-2859
defensive cell1.35e-2748
phagocyte1.35e-2748
classical monocyte5.50e-2642
CD14-positive, CD16-negative classical monocyte5.50e-2642
leukocyte2.24e-20136
hematopoietic lineage restricted progenitor cell1.79e-18120
myeloid cell1.99e-18108
common myeloid progenitor1.99e-18108
nongranular leukocyte8.65e-17115
stuff accumulating cell7.65e-1587
hematopoietic stem cell1.31e-14168
angioblastic mesenchymal cell1.31e-14168
mesenchymal cell2.84e-14354
hematopoietic cell1.18e-13177
hematopoietic oligopotent progenitor cell4.67e-13161
hematopoietic multipotent progenitor cell4.67e-13161
connective tissue cell5.06e-13361
motile cell7.51e-11386
multi fate stem cell4.72e-10427
somatic stem cell1.39e-08433
stem cell5.96e-08441
Uber Anatomy
Ontology termp-valuen
bone marrow1.37e-2776
bone element1.26e-2582
hematopoietic system1.69e-2498
blood island1.69e-2498
immune system2.08e-2393
hemolymphoid system2.82e-22108
skeletal element1.29e-1990
skeletal system1.43e-17100
adult organism2.82e-14114
connective tissue6.98e-13371
lateral plate mesoderm1.70e-10203
musculoskeletal system8.77e-10167
mesoderm2.33e-08315
mesoderm-derived structure2.33e-08315
presumptive mesoderm2.33e-08315
tissue1.50e-07773


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
BCLAF1#9774214.43509840674790.006201147435546130.0273797935664582
CCNT2#90536.336201576962630.003930750035764890.0189670857043638
E2F1#186934.907389214879320.008460985347239390.0324539756383258
ELF1#199734.258097958807540.01295179875054610.0461222350555197
PBX3#5090214.60967512449610.006056122473217890.0268199709528221
SIN3A#2594235.408884726815140.006318961977991520.0276035665894034
TCF12#6938310.63446490218640.0008313523990202070.006287155191982



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.