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Coexpression cluster:C2301: Difference between revisions

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|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_celltype=CL:0002194!3.42e-52!59;CL:0000576!3.42e-52!59;CL:0000040!3.42e-52!59;CL:0000559!3.42e-52!59;CL:0002009!1.08e-51!61;CL:0000473!2.70e-51!48;CL:0000234!2.70e-51!48;CL:0002087!2.43e-48!115;CL:0000738!1.01e-47!136;CL:0000766!1.93e-46!72;CL:0000557!4.69e-45!67;CL:0000860!5.32e-45!42;CL:0002057!5.32e-45!42;CL:0000839!2.60e-44!66;CL:0002031!8.28e-42!120;CL:0000037!1.87e-32!168;CL:0000566!1.87e-32!168;CL:0000988!9.96e-32!177;CL:0002032!1.06e-31!161;CL:0000837!1.06e-31!161;CL:0000763!2.29e-28!108;CL:0000049!2.29e-28!108;CL:0000325!1.13e-19!87;CL:0002393!1.35e-11!9;CL:0002397!1.35e-11!9;CL:0000990!4.42e-08!8;CL:0000235!1.59e-07!6
|ontology_enrichment_disease=
|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
|ontology_enrichment_uberon=UBERON:0002390!8.79e-51!98;UBERON:0003061!8.79e-51!98;UBERON:0002193!1.14e-46!108;UBERON:0002371!7.27e-39!76;UBERON:0002405!1.59e-34!93;UBERON:0001474!2.14e-34!82;UBERON:0004765!2.10e-29!90;UBERON:0001434!2.09e-25!100;UBERON:0007023!1.36e-24!114;UBERON:0003081!3.05e-20!203;UBERON:0000178!1.62e-13!15;UBERON:0000179!1.62e-13!15;UBERON:0000463!1.62e-13!15;UBERON:0002204!3.73e-13!167;UBERON:0000926!1.92e-09!315;UBERON:0004120!1.92e-09!315;UBERON:0006603!1.92e-09!315;UBERON:0000479!1.96e-07!773
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}}
}}

Revision as of 13:51, 19 October 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
monopoietic cell3.42e-5259
monocyte3.42e-5259
monoblast3.42e-5259
promonocyte3.42e-5259
macrophage dendritic cell progenitor1.08e-5161
defensive cell2.70e-5148
phagocyte2.70e-5148
nongranular leukocyte2.43e-48115
leukocyte1.01e-47136
myeloid leukocyte1.93e-4672
granulocyte monocyte progenitor cell4.69e-4567
classical monocyte5.32e-4542
CD14-positive, CD16-negative classical monocyte5.32e-4542
myeloid lineage restricted progenitor cell2.60e-4466
hematopoietic lineage restricted progenitor cell8.28e-42120
hematopoietic stem cell1.87e-32168
angioblastic mesenchymal cell1.87e-32168
hematopoietic cell9.96e-32177
hematopoietic oligopotent progenitor cell1.06e-31161
hematopoietic multipotent progenitor cell1.06e-31161
myeloid cell2.29e-28108
common myeloid progenitor2.29e-28108
stuff accumulating cell1.13e-1987
intermediate monocyte1.35e-119
CD14-positive, CD16-positive monocyte1.35e-119
conventional dendritic cell4.42e-088
macrophage1.59e-076
Uber Anatomy
Ontology termp-valuen
hematopoietic system8.79e-5198
blood island8.79e-5198
hemolymphoid system1.14e-46108
bone marrow7.27e-3976
immune system1.59e-3493
bone element2.14e-3482
skeletal element2.10e-2990
skeletal system2.09e-25100
adult organism1.36e-24114
lateral plate mesoderm3.05e-20203
blood1.62e-1315
haemolymphatic fluid1.62e-1315
organism substance1.62e-1315
musculoskeletal system3.73e-13167
mesoderm1.92e-09315
mesoderm-derived structure1.92e-09315
presumptive mesoderm1.92e-09315
tissue1.96e-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


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.