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Coexpression cluster:C2365: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0002390!7.40e-51!98;UBERON:0003061!7.40e-51!98;UBERON:0002193!4.53e-46!108;UBERON:0002371!6.34e-42!76;UBERON:0002405!1.92e-38!93;UBERON:0001474!6.42e-37!82;UBERON:0007023!3.25e-36!114;UBERON:0004765!2.46e-31!90;UBERON:0001434!1.68e-27!100;UBERON:0003081!1.55e-17!203;UBERON:0002204!1.96e-11!167;UBERON:0001049!9.48e-11!56;UBERON:0005068!9.48e-11!56;UBERON:0006241!9.48e-11!56;UBERON:0007135!9.48e-11!56;UBERON:0000073!1.92e-09!53;UBERON:0002616!1.92e-09!53;UBERON:0000479!2.23e-09!773;UBERON:0002780!4.12e-08!41;UBERON:0001890!4.12e-08!41;UBERON:0003080!4.12e-08!41;UBERON:0006240!4.12e-08!41;UBERON:0000178!4.78e-08!15;UBERON:0000179!4.78e-08!15;UBERON:0000463!4.78e-08!15;UBERON:0000926!3.99e-07!315;UBERON:0004120!3.99e-07!315;UBERON:0006603!3.99e-07!315;UBERON:0000923!5.74e-07!560;UBERON:0010316!5.74e-07!560;UBERON:0005291!5.74e-07!560;UBERON:0006598!5.74e-07!560;UBERON:0010317!5.74e-07!560;UBERON:0002532!5.74e-07!560;UBERON:0001893!6.30e-07!34;UBERON:0003528!7.46e-07!34;UBERON:0002020!7.46e-07!34
|ontology_enrichment_uberon=UBERON:0002390!7.40e-51!98;UBERON:0003061!7.40e-51!98;UBERON:0002193!4.53e-46!108;UBERON:0002371!6.34e-42!76;UBERON:0002405!1.92e-38!93;UBERON:0001474!6.42e-37!82;UBERON:0007023!3.25e-36!114;UBERON:0004765!2.46e-31!90;UBERON:0001434!1.68e-27!100;UBERON:0003081!1.55e-17!203;UBERON:0002204!1.96e-11!167;UBERON:0001049!9.48e-11!56;UBERON:0005068!9.48e-11!56;UBERON:0006241!9.48e-11!56;UBERON:0007135!9.48e-11!56;UBERON:0000073!1.92e-09!53;UBERON:0002616!1.92e-09!53;UBERON:0000479!2.23e-09!773;UBERON:0002780!4.12e-08!41;UBERON:0001890!4.12e-08!41;UBERON:0003080!4.12e-08!41;UBERON:0006240!4.12e-08!41;UBERON:0000178!4.78e-08!15;UBERON:0000179!4.78e-08!15;UBERON:0000463!4.78e-08!15;UBERON:0000926!3.99e-07!315;UBERON:0004120!3.99e-07!315;UBERON:0006603!3.99e-07!315;UBERON:0000923!5.74e-07!560;UBERON:0010316!5.74e-07!560;UBERON:0005291!5.74e-07!560;UBERON:0006598!5.74e-07!560;UBERON:0010317!5.74e-07!560;UBERON:0002532!5.74e-07!560;UBERON:0001893!6.30e-07!34;UBERON:0003528!7.46e-07!34;UBERON:0002020!7.46e-07!34
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}}
}}

Revision as of 15:27, 26 November 2012


Full id: C2365_CD14_Dendritic_Macrophage_Monocytederived_Neutrophils_Eosinophils_Whole



Phase1 CAGE Peaks

Hg19::chr16:21663919..21663936,-p1@IGSF6
Hg19::chr16:21663950..21663959,-p2@IGSF6
Hg19::chr7:150478190..150478222,-p1@uc003whs.1
Hg19::chrX:119438243..119438304,-p@chrX:119438243..119438304
-


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

No GOStat results

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 leukocyte2.11e-5672
macrophage dendritic cell progenitor1.14e-5561
monopoietic cell2.68e-5459
monocyte2.68e-5459
monoblast2.68e-5459
promonocyte2.68e-5459
granulocyte monocyte progenitor cell3.46e-5167
defensive cell5.11e-4848
phagocyte5.11e-4848
myeloid lineage restricted progenitor cell4.82e-4766
myeloid cell6.40e-45108
common myeloid progenitor6.40e-45108
leukocyte4.83e-43136
classical monocyte1.09e-4142
CD14-positive, CD16-negative classical monocyte1.09e-4142
hematopoietic stem cell3.77e-36168
angioblastic mesenchymal cell3.77e-36168
nongranular leukocyte1.17e-34115
hematopoietic oligopotent progenitor cell1.08e-33161
hematopoietic multipotent progenitor cell1.08e-33161
hematopoietic cell2.19e-32177
hematopoietic lineage restricted progenitor cell1.48e-30120
stuff accumulating cell1.53e-1987
dendritic cell8.75e-1010
intermediate monocyte6.15e-099
CD14-positive, CD16-positive monocyte6.15e-099
conventional dendritic cell1.78e-088
granulocyte5.63e-088
macrophage1.39e-076
Uber Anatomy
Ontology termp-valuen
hematopoietic system7.40e-5198
blood island7.40e-5198
hemolymphoid system4.53e-46108
bone marrow6.34e-4276
immune system1.92e-3893
bone element6.42e-3782
adult organism3.25e-36114
skeletal element2.46e-3190
skeletal system1.68e-27100
lateral plate mesoderm1.55e-17203
musculoskeletal system1.96e-11167
neural tube9.48e-1156
neural rod9.48e-1156
future spinal cord9.48e-1156
neural keel9.48e-1156
regional part of nervous system1.92e-0953
regional part of brain1.92e-0953
tissue2.23e-09773
regional part of forebrain4.12e-0841
forebrain4.12e-0841
anterior neural tube4.12e-0841
future forebrain4.12e-0841
blood4.78e-0815
haemolymphatic fluid4.78e-0815
organism substance4.78e-0815
mesoderm3.99e-07315
mesoderm-derived structure3.99e-07315
presumptive mesoderm3.99e-07315
germ layer5.74e-07560
germ layer / neural crest5.74e-07560
embryonic tissue5.74e-07560
presumptive structure5.74e-07560
germ layer / neural crest derived structure5.74e-07560
epiblast (generic)5.74e-07560
telencephalon6.30e-0734
brain grey matter7.46e-0734
gray matter7.46e-0734


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.

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