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Coexpression cluster:C303: Difference between revisions

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|gostat_on_coexpression_clusters=GO:0019841!retinol binding!0.00425250120614753!116362$GO:0016918!retinal binding!0.00425250120614753!116362$GO:0005501!retinoid binding!0.00425250120614753!116362$GO:0019840!isoprenoid binding!0.00425250120614753!116362$GO:0005625!soluble fraction!0.0407202229474492!3957$GO:0019842!vitamin binding!0.0407202229474492!116362$GO:0005529!sugar binding!0.0493596312651508!3957
|gostat_on_coexpression_clusters=GO:0019841!retinol binding!0.00425250120614753!116362$GO:0016918!retinal binding!0.00425250120614753!116362$GO:0005501!retinoid binding!0.00425250120614753!116362$GO:0019840!isoprenoid binding!0.00425250120614753!116362$GO:0005625!soluble fraction!0.0407202229474492!3957$GO:0019842!vitamin binding!0.0407202229474492!116362$GO:0005529!sugar binding!0.0493596312651508!3957
|id=C303
|id=C303
|ontology_enrichment_celltype=CL:0000766!6.29e-35!76;CL:0000738!3.14e-34!140;CL:0000557!2.35e-31!71;CL:0002009!4.98e-31!65;CL:0002194!4.86e-30!63;CL:0000576!4.86e-30!63;CL:0000040!4.86e-30!63;CL:0000559!4.86e-30!63;CL:0000037!1.35e-29!172;CL:0000566!1.35e-29!172;CL:0000839!2.09e-29!70;CL:0002057!7.82e-28!42;CL:0000763!3.63e-27!112;CL:0000049!3.63e-27!112;CL:0002031!4.00e-27!124;CL:0002087!6.15e-27!119;CL:0000988!7.34e-27!182;CL:0002032!1.63e-26!165;CL:0000837!1.63e-26!165;CL:0000860!5.83e-24!45;CL:0002393!1.64e-07!9;CL:0002397!1.64e-07!9
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002390!8.39e-35!102;UBERON:0003061!8.39e-35!102;UBERON:0002193!7.06e-32!112;UBERON:0002371!2.41e-28!80;UBERON:0001474!8.15e-26!86;UBERON:0007023!1.32e-25!115;UBERON:0002405!9.76e-25!115;UBERON:0004765!2.57e-19!101;UBERON:0001434!2.57e-19!101;UBERON:0003081!1.87e-14!216;UBERON:0001049!1.42e-08!57;UBERON:0005068!1.42e-08!57;UBERON:0006241!1.42e-08!57;UBERON:0007135!1.42e-08!57;UBERON:0002204!2.98e-07!167;UBERON:0000479!5.78e-07!787;UBERON:0003080!9.73e-07!42
}}
}}

Revision as of 14:31, 21 May 2012


Full id: C303_CD14_Basophils_Peripheral_Eosinophils_CD14CD16_Neutrophils_Whole



Phase1 CAGE Peaks

Hg19::chr10:135073029..135073042,+p@chr10:135073029..135073042
+
Hg19::chr11:64163297..64163310,-p1@ENST00000457725
Hg19::chr11:65220998..65221001,+p@chr11:65220998..65221001
+
Hg19::chr11:66888450..66888468,-p@chr11:66888450..66888468
-
Hg19::chr12:69747591..69747611,-p1@ENST00000548626
Hg19::chr13:99922932..99922946,-p@chr13:99922932..99922946
-
Hg19::chr13:99930136..99930140,+p1@AF339795
Hg19::chr13:99932682..99932704,+p@chr13:99932682..99932704
+
Hg19::chr13:99932706..99932716,+p@chr13:99932706..99932716
+
Hg19::chr13:99934075..99934096,-p@chr13:99934075..99934096
-
Hg19::chr14:75754624..75754635,+p@chr14:75754624..75754635
+
Hg19::chr17:7024749..7024764,-p@chr17:7024749..7024764
-
Hg19::chr17:7077590..7077615,-p@chr17:7077590..7077615
-
Hg19::chr17:7077620..7077625,-p@chr17:7077620..7077625
-
Hg19::chr17:72524949..72524975,+p@chr17:72524949..72524975
+
Hg19::chr17:72774120..72774160,-p@chr17:72774120..72774160
-
Hg19::chr17:72776484..72776500,+p@chr17:72776484..72776500
+
Hg19::chr17:72776516..72776526,+p@chr17:72776516..72776526
+
Hg19::chr17:81060279..81060283,-p@chr17:81060279..81060283
-
Hg19::chr17:81101323..81101338,+p@chr17:81101323..81101338
+
Hg19::chr17:81103271..81103285,-p@chr17:81103271..81103285
-
Hg19::chr17:81103526..81103542,+p@chr17:81103526..81103542
+
Hg19::chr17:81147900..81147911,+p@chr17:81147900..81147911
+
Hg19::chr1:10057123..10057149,+p3@RBP7
Hg19::chr22:37976067..37976079,-p3@LGALS2
Hg19::chr2:230162106..230162117,-p@chr2:230162106..230162117
-
Hg19::chr2:230162122..230162143,-p@chr2:230162122..230162143
-
Hg19::chr5:139631154..139631161,-p@chr5:139631154..139631161
-
Hg19::chr5:139725653..139725678,-p@chr5:139725653..139725678
-
Hg19::chr6:11537600..11537651,-p@chr6:11537600..11537651
-
Hg19::chr6:163826254..163826261,+p@chr6:163826254..163826261
+
Hg19::chr6:163827012..163827025,-p@chr6:163827012..163827025
-
Hg19::chr7:2774708..2774727,-p@chr7:2774708..2774727
-
Hg19::chr7:2797828..2797848,-p@chr7:2797828..2797848
-
Hg19::chr8:48273366..48273391,+p3@KIAA0146
Hg19::chr8:48273416..48273419,+p15@KIAA0146
Hg19::chr8:48282088..48282092,-p@chr8:48282088..48282092
-
Hg19::chr8:48513543..48513562,+p@chr8:48513543..48513562
+
Hg19::chr8:48540690..48540694,+p@chr8:48540690..48540694
+
Hg19::chr9:27701766..27701787,-p@chr9:27701766..27701787
-


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:0019841retinol binding0.00425250120614753
GO:0016918retinal binding0.00425250120614753
GO:0005501retinoid binding0.00425250120614753
GO:0019840isoprenoid binding0.00425250120614753
GO:0005625soluble fraction0.0407202229474492
GO:0019842vitamin binding0.0407202229474492
GO:0005529sugar binding0.0493596312651508



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 leukocyte6.29e-3576
leukocyte3.14e-34140
granulocyte monocyte progenitor cell2.35e-3171
macrophage dendritic cell progenitor4.98e-3165
monopoietic cell4.86e-3063
monocyte4.86e-3063
monoblast4.86e-3063
promonocyte4.86e-3063
hematopoietic stem cell1.35e-29172
angioblastic mesenchymal cell1.35e-29172
myeloid lineage restricted progenitor cell2.09e-2970
CD14-positive, CD16-negative classical monocyte7.82e-2842
myeloid cell3.63e-27112
common myeloid progenitor3.63e-27112
hematopoietic lineage restricted progenitor cell4.00e-27124
nongranular leukocyte6.15e-27119
hematopoietic cell7.34e-27182
hematopoietic oligopotent progenitor cell1.63e-26165
hematopoietic multipotent progenitor cell1.63e-26165
classical monocyte5.83e-2445
intermediate monocyte1.64e-079
CD14-positive, CD16-positive monocyte1.64e-079
Uber Anatomy
Ontology termp-valuen
hematopoietic system8.39e-35102
blood island8.39e-35102
hemolymphoid system7.06e-32112
bone marrow2.41e-2880
bone element8.15e-2686
adult organism1.32e-25115
immune system9.76e-25115
skeletal element2.57e-19101
skeletal system2.57e-19101
lateral plate mesoderm1.87e-14216
neural tube1.42e-0857
neural rod1.42e-0857
future spinal cord1.42e-0857
neural keel1.42e-0857
musculoskeletal system2.98e-07167
tissue5.78e-07787
anterior neural tube9.73e-0742


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


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