Personal tools

Coexpression cluster:C2301: Difference between revisions

From FANTOM5_SSTAR

Jump to: navigation, search
No edit summary
No edit summary
Line 3: Line 3:
|gostat_on_coexpression_clusters=GO:0030371!translation repressor activity!0.00618156128576475!23034$GO:0045727!positive regulation of translation!0.0150123631225715!23034$GO:0031328!positive regulation of cellular biosynthetic process!0.0150123631225715!23034$GO:0009891!positive regulation of biosynthetic process!0.0150123631225715!23034$GO:0051247!positive regulation of protein metabolic process!0.0150123631225715!23034$GO:0006417!regulation of translation!0.0239535499823384!23034$GO:0031326!regulation of cellular biosynthetic process!0.0239535499823384!23034$GO:0009889!regulation of biosynthetic process!0.0239535499823384!23034$GO:0031325!positive regulation of cellular metabolic process!0.0338781670466587!23034$GO:0009893!positive regulation of metabolic process!0.0338781670466587!23034$GO:0051246!regulation of protein metabolic process!0.0338781670466587!23034
|gostat_on_coexpression_clusters=GO:0030371!translation repressor activity!0.00618156128576475!23034$GO:0045727!positive regulation of translation!0.0150123631225715!23034$GO:0031328!positive regulation of cellular biosynthetic process!0.0150123631225715!23034$GO:0009891!positive regulation of biosynthetic process!0.0150123631225715!23034$GO:0051247!positive regulation of protein metabolic process!0.0150123631225715!23034$GO:0006417!regulation of translation!0.0239535499823384!23034$GO:0031326!regulation of cellular biosynthetic process!0.0239535499823384!23034$GO:0009889!regulation of biosynthetic process!0.0239535499823384!23034$GO:0031325!positive regulation of cellular metabolic process!0.0338781670466587!23034$GO:0009893!positive regulation of metabolic process!0.0338781670466587!23034$GO:0051246!regulation of protein metabolic process!0.0338781670466587!23034
|id=C2301
|id=C2301
|ontology_enrichment_celltype=CL:0000738!6.35e-41!140;CL:0002087!2.72e-36!119;CL:0000766!3.11e-33!76;CL:0002057!6.31e-32!42;CL:0002031!9.92e-32!124;CL:0002194!2.37e-31!63;CL:0000576!2.37e-31!63;CL:0000040!2.37e-31!63;CL:0000559!2.37e-31!63;CL:0002009!6.42e-31!65;CL:0000860!3.18e-28!45;CL:0000037!6.15e-28!172;CL:0000566!6.15e-28!172;CL:0000557!2.04e-27!71;CL:0000839!6.43e-27!70;CL:0002032!3.78e-26!165;CL:0000837!3.78e-26!165;CL:0000988!4.58e-26!182;CL:0000763!1.61e-19!112;CL:0000049!1.61e-19!112;CL:0002393!1.43e-08!9;CL:0002397!1.43e-08!9;CL:0000838!6.08e-07!52
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002390!2.02e-34!102;UBERON:0003061!2.02e-34!102;UBERON:0002193!5.61e-31!112;UBERON:0007023!2.50e-30!115;UBERON:0002371!9.78e-26!80;UBERON:0001474!1.33e-22!86;UBERON:0002405!3.40e-19!115;UBERON:0004765!1.66e-17!101;UBERON:0001434!1.66e-17!101;UBERON:0003081!1.73e-14!216;UBERON:0002204!7.72e-13!167;UBERON:0000178!3.22e-10!15;UBERON:0000179!3.22e-10!15;UBERON:0000463!3.22e-10!15;UBERON:0001049!1.81e-07!57;UBERON:0005068!1.81e-07!57;UBERON:0006241!1.81e-07!57;UBERON:0007135!1.81e-07!57
}}
}}

Revision as of 14:22, 21 May 2012


Full id: C2301_CD14CD16_CD14_migratory_Dendritic_Basophils_Macrophage_myeloma



Phase1 CAGE Peaks

Hg19::chr14:55243185..55243200,+p16@SAMD4A
Hg19::chr1:40810464..40810514,+p2@SMAP2
Hg19::chr1:40810516..40810538,+p5@SMAP2
Hg19::chr1:40811665..40811670,+p@chr1:40811665..40811670
+


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:0030371translation repressor activity0.00618156128576475
GO:0045727positive regulation of translation0.0150123631225715
GO:0031328positive regulation of cellular biosynthetic process0.0150123631225715
GO:0009891positive regulation of biosynthetic process0.0150123631225715
GO:0051247positive regulation of protein metabolic process0.0150123631225715
GO:0006417regulation of translation0.0239535499823384
GO:0031326regulation of cellular biosynthetic process0.0239535499823384
GO:0009889regulation of biosynthetic process0.0239535499823384
GO:0031325positive regulation of cellular metabolic process0.0338781670466587
GO:0009893positive regulation of metabolic process0.0338781670466587
GO:0051246regulation of protein metabolic process0.0338781670466587



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
leukocyte6.35e-41140
nongranular leukocyte2.72e-36119
myeloid leukocyte3.11e-3376
CD14-positive, CD16-negative classical monocyte6.31e-3242
hematopoietic lineage restricted progenitor cell9.92e-32124
monopoietic cell2.37e-3163
monocyte2.37e-3163
monoblast2.37e-3163
promonocyte2.37e-3163
macrophage dendritic cell progenitor6.42e-3165
classical monocyte3.18e-2845
hematopoietic stem cell6.15e-28172
angioblastic mesenchymal cell6.15e-28172
granulocyte monocyte progenitor cell2.04e-2771
myeloid lineage restricted progenitor cell6.43e-2770
hematopoietic oligopotent progenitor cell3.78e-26165
hematopoietic multipotent progenitor cell3.78e-26165
hematopoietic cell4.58e-26182
myeloid cell1.61e-19112
common myeloid progenitor1.61e-19112
intermediate monocyte1.43e-089
CD14-positive, CD16-positive monocyte1.43e-089
lymphoid lineage restricted progenitor cell6.08e-0752
Uber Anatomy
Ontology termp-valuen
hematopoietic system2.02e-34102
blood island2.02e-34102
hemolymphoid system5.61e-31112
adult organism2.50e-30115
bone marrow9.78e-2680
bone element1.33e-2286
immune system3.40e-19115
skeletal element1.66e-17101
skeletal system1.66e-17101
lateral plate mesoderm1.73e-14216
musculoskeletal system7.72e-13167
blood3.22e-1015
haemolymphatic fluid3.22e-1015
organism substance3.22e-1015
neural tube1.81e-0757
neural rod1.81e-0757
future spinal cord1.81e-0757
neural keel1.81e-0757


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.