Personal tools

Coexpression cluster:C3790: 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:0003938!IMP dehydrogenase activity!0.0128031549908582!3614$GO:0046037!GMP metabolic process!0.0128031549908582!3614$GO:0006177!GMP biosynthetic process!0.0128031549908582!3614$GO:0009168!purine ribonucleoside monophosphate biosynthetic process!0.0224329571967736!3614$GO:0009167!purine ribonucleoside monophosphate metabolic process!0.0224329571967736!3614$GO:0009127!purine nucleoside monophosphate biosynthetic process!0.0224329571967736!3614$GO:0009126!purine nucleoside monophosphate metabolic process!0.0224329571967736!3614$GO:0009161!ribonucleoside monophosphate metabolic process!0.0224329571967736!3614$GO:0009156!ribonucleoside monophosphate biosynthetic process!0.0224329571967736!3614$GO:0006183!GTP biosynthetic process!0.0224329571967736!3614$GO:0046039!GTP metabolic process!0.0224329571967736!3614$GO:0009124!nucleoside monophosphate biosynthetic process!0.0224329571967736!3614$GO:0009123!nucleoside monophosphate metabolic process!0.0224329571967736!3614$GO:0009206!purine ribonucleoside triphosphate biosynthetic process!0.0403744453611115!3614$GO:0009145!purine nucleoside triphosphate biosynthetic process!0.0403744453611115!3614$GO:0009201!ribonucleoside triphosphate biosynthetic process!0.0403744453611115!3614$GO:0008076!voltage-gated potassium channel complex!0.0403744453611115!92799$GO:0009142!nucleoside triphosphate biosynthetic process!0.0403744453611115!3614$GO:0009205!purine ribonucleoside triphosphate metabolic process!0.0403744453611115!3614$GO:0009144!purine nucleoside triphosphate metabolic process!0.0403744453611115!3614$GO:0009199!ribonucleoside triphosphate metabolic process!0.0403744453611115!3614$GO:0030955!potassium ion binding!0.0403744453611115!3614$GO:0009152!purine ribonucleotide biosynthetic process!0.0403744453611115!3614$GO:0009141!nucleoside triphosphate metabolic process!0.0403744453611115!3614$GO:0016616!oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor!0.0403744453611115!3614$GO:0009150!purine ribonucleotide metabolic process!0.0403744453611115!3614$GO:0009260!ribonucleotide biosynthetic process!0.0403744453611115!3614$GO:0006164!purine nucleotide biosynthetic process!0.0403744453611115!3614$GO:0016614!oxidoreductase activity, acting on CH-OH group of donors!0.0403744453611115!3614$GO:0005249!voltage-gated potassium channel activity!0.0403744453611115!92799$GO:0006163!purine nucleotide metabolic process!0.0403744453611115!3614$GO:0009259!ribonucleotide metabolic process!0.0403744453611115!3614$GO:0005267!potassium channel activity!0.0472803330340079!92799$GO:0031420!alkali metal ion binding!0.0472803330340079!3614$GO:0007601!visual perception!0.0472803330340079!3614$GO:0050953!sensory perception of light stimulus!0.0472803330340079!3614
|gostat_on_coexpression_clusters=GO:0003938!IMP dehydrogenase activity!0.0128031549908582!3614$GO:0046037!GMP metabolic process!0.0128031549908582!3614$GO:0006177!GMP biosynthetic process!0.0128031549908582!3614$GO:0009168!purine ribonucleoside monophosphate biosynthetic process!0.0224329571967736!3614$GO:0009167!purine ribonucleoside monophosphate metabolic process!0.0224329571967736!3614$GO:0009127!purine nucleoside monophosphate biosynthetic process!0.0224329571967736!3614$GO:0009126!purine nucleoside monophosphate metabolic process!0.0224329571967736!3614$GO:0009161!ribonucleoside monophosphate metabolic process!0.0224329571967736!3614$GO:0009156!ribonucleoside monophosphate biosynthetic process!0.0224329571967736!3614$GO:0006183!GTP biosynthetic process!0.0224329571967736!3614$GO:0046039!GTP metabolic process!0.0224329571967736!3614$GO:0009124!nucleoside monophosphate biosynthetic process!0.0224329571967736!3614$GO:0009123!nucleoside monophosphate metabolic process!0.0224329571967736!3614$GO:0009206!purine ribonucleoside triphosphate biosynthetic process!0.0403744453611115!3614$GO:0009145!purine nucleoside triphosphate biosynthetic process!0.0403744453611115!3614$GO:0009201!ribonucleoside triphosphate biosynthetic process!0.0403744453611115!3614$GO:0008076!voltage-gated potassium channel complex!0.0403744453611115!92799$GO:0009142!nucleoside triphosphate biosynthetic process!0.0403744453611115!3614$GO:0009205!purine ribonucleoside triphosphate metabolic process!0.0403744453611115!3614$GO:0009144!purine nucleoside triphosphate metabolic process!0.0403744453611115!3614$GO:0009199!ribonucleoside triphosphate metabolic process!0.0403744453611115!3614$GO:0030955!potassium ion binding!0.0403744453611115!3614$GO:0009152!purine ribonucleotide biosynthetic process!0.0403744453611115!3614$GO:0009141!nucleoside triphosphate metabolic process!0.0403744453611115!3614$GO:0016616!oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor!0.0403744453611115!3614$GO:0009150!purine ribonucleotide metabolic process!0.0403744453611115!3614$GO:0009260!ribonucleotide biosynthetic process!0.0403744453611115!3614$GO:0006164!purine nucleotide biosynthetic process!0.0403744453611115!3614$GO:0016614!oxidoreductase activity, acting on CH-OH group of donors!0.0403744453611115!3614$GO:0005249!voltage-gated potassium channel activity!0.0403744453611115!92799$GO:0006163!purine nucleotide metabolic process!0.0403744453611115!3614$GO:0009259!ribonucleotide metabolic process!0.0403744453611115!3614$GO:0005267!potassium channel activity!0.0472803330340079!92799$GO:0031420!alkali metal ion binding!0.0472803330340079!3614$GO:0007601!visual perception!0.0472803330340079!3614$GO:0050953!sensory perception of light stimulus!0.0472803330340079!3614
|id=C3790
|id=C3790
|ontology_enrichment_celltype=CL:0002087!2.46e-28!119;CL:0000738!2.42e-27!140;CL:0002371!2.25e-26!591;CL:0002194!6.72e-26!63;CL:0000576!6.72e-26!63;CL:0000040!6.72e-26!63;CL:0000559!6.72e-26!63;CL:0002009!1.06e-25!65;CL:0000766!3.15e-25!76;CL:0002057!1.86e-24!42;CL:0002031!3.92e-21!124;CL:0000037!4.11e-21!172;CL:0000566!4.11e-21!172;CL:0000557!8.21e-21!71;CL:0000988!8.55e-21!182;CL:0002032!9.68e-21!165;CL:0000837!9.68e-21!165;CL:0000860!1.25e-20!45;CL:0000144!2.11e-20!625;CL:0000839!1.85e-18!70;CL:0000003!4.03e-18!722;CL:0000723!1.12e-16!436;CL:0000048!1.35e-16!430;CL:0000763!1.90e-16!112;CL:0000049!1.90e-16!112;CL:0002320!2.40e-16!365;CL:0000134!3.00e-15!358;CL:0000034!3.06e-15!444;CL:0000219!7.87e-13!390;CL:0000548!4.32e-10!679;CL:0000004!4.32e-10!679;CL:0000255!4.32e-10!679;CL:0000012!6.07e-10!682;CL:0000063!5.36e-09!578;CL:0002393!4.19e-07!9;CL:0002397!4.19e-07!9
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0003081!5.78e-28!216;UBERON:0002390!4.22e-25!102;UBERON:0003061!4.22e-25!102;UBERON:0002193!1.50e-24!112;UBERON:0002371!1.01e-20!80;UBERON:0001474!1.76e-18!86;UBERON:0002384!2.04e-15!375;UBERON:0004765!3.94e-15!101;UBERON:0001434!3.94e-15!101;UBERON:0002405!7.31e-15!115;UBERON:0002204!1.11e-14!167
}}
}}

Revision as of 14:40, 21 May 2012


Full id: C3790_Neutrophils_Eosinophils_Mesenchymal_Whole_Alveolar_blood_CD14



Phase1 CAGE Peaks

Hg19::chr19:41082755..41082801,+p1@SHKBP1
Hg19::chr7:100450328..100450398,+p1@SLC12A9
Hg19::chr7:128050027..128050053,-p2@IMPDH1


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:0003938IMP dehydrogenase activity0.0128031549908582
GO:0046037GMP metabolic process0.0128031549908582
GO:0006177GMP biosynthetic process0.0128031549908582
GO:0009168purine ribonucleoside monophosphate biosynthetic process0.0224329571967736
GO:0009167purine ribonucleoside monophosphate metabolic process0.0224329571967736
GO:0009127purine nucleoside monophosphate biosynthetic process0.0224329571967736
GO:0009126purine nucleoside monophosphate metabolic process0.0224329571967736
GO:0009161ribonucleoside monophosphate metabolic process0.0224329571967736
GO:0009156ribonucleoside monophosphate biosynthetic process0.0224329571967736
GO:0006183GTP biosynthetic process0.0224329571967736
GO:0046039GTP metabolic process0.0224329571967736
GO:0009124nucleoside monophosphate biosynthetic process0.0224329571967736
GO:0009123nucleoside monophosphate metabolic process0.0224329571967736
GO:0009206purine ribonucleoside triphosphate biosynthetic process0.0403744453611115
GO:0009145purine nucleoside triphosphate biosynthetic process0.0403744453611115
GO:0009201ribonucleoside triphosphate biosynthetic process0.0403744453611115
GO:0008076voltage-gated potassium channel complex0.0403744453611115
GO:0009142nucleoside triphosphate biosynthetic process0.0403744453611115
GO:0009205purine ribonucleoside triphosphate metabolic process0.0403744453611115
GO:0009144purine nucleoside triphosphate metabolic process0.0403744453611115
GO:0009199ribonucleoside triphosphate metabolic process0.0403744453611115
GO:0030955potassium ion binding0.0403744453611115
GO:0009152purine ribonucleotide biosynthetic process0.0403744453611115
GO:0009141nucleoside triphosphate metabolic process0.0403744453611115
GO:0016616oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor0.0403744453611115
GO:0009150purine ribonucleotide metabolic process0.0403744453611115
GO:0009260ribonucleotide biosynthetic process0.0403744453611115
GO:0006164purine nucleotide biosynthetic process0.0403744453611115
GO:0016614oxidoreductase activity, acting on CH-OH group of donors0.0403744453611115
GO:0005249voltage-gated potassium channel activity0.0403744453611115
GO:0006163purine nucleotide metabolic process0.0403744453611115
GO:0009259ribonucleotide metabolic process0.0403744453611115
GO:0005267potassium channel activity0.0472803330340079
GO:0031420alkali metal ion binding0.0472803330340079
GO:0007601visual perception0.0472803330340079
GO:0050953sensory perception of light stimulus0.0472803330340079



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
nongranular leukocyte2.46e-28119
leukocyte2.42e-27140
somatic cell2.25e-26591
monopoietic cell6.72e-2663
monocyte6.72e-2663
monoblast6.72e-2663
promonocyte6.72e-2663
macrophage dendritic cell progenitor1.06e-2565
myeloid leukocyte3.15e-2576
CD14-positive, CD16-negative classical monocyte1.86e-2442
hematopoietic lineage restricted progenitor cell3.92e-21124
hematopoietic stem cell4.11e-21172
angioblastic mesenchymal cell4.11e-21172
granulocyte monocyte progenitor cell8.21e-2171
hematopoietic cell8.55e-21182
hematopoietic oligopotent progenitor cell9.68e-21165
hematopoietic multipotent progenitor cell9.68e-21165
classical monocyte1.25e-2045
myeloid lineage restricted progenitor cell1.85e-1870
native cell4.03e-18722
somatic stem cell1.12e-16436
multi fate stem cell1.35e-16430
myeloid cell1.90e-16112
common myeloid progenitor1.90e-16112
connective tissue cell2.40e-16365
mesenchymal cell3.00e-15358
stem cell3.06e-15444
motile cell7.87e-13390
animal cell4.32e-10679
eukaryotic cell4.32e-10679
intermediate monocyte4.19e-079
CD14-positive, CD16-positive monocyte4.19e-079
Uber Anatomy
Ontology termp-valuen
lateral plate mesoderm5.78e-28216
hematopoietic system4.22e-25102
blood island4.22e-25102
hemolymphoid system1.50e-24112
bone marrow1.01e-2080
bone element1.76e-1886
connective tissue2.04e-15375
skeletal element3.94e-15101
skeletal system3.94e-15101
immune system7.31e-15115
musculoskeletal system1.11e-14167


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.

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=Coexpression_cluster:C3790&oldid=1706697"