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Coexpression cluster:C1988: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0007023!1.15e-44!115;UBERON:0002390!8.62e-27!102;UBERON:0003061!8.62e-27!102;UBERON:0002193!8.98e-25!112;UBERON:0002371!2.94e-24!80;UBERON:0002405!1.42e-21!115;UBERON:0001474!6.77e-21!86;UBERON:0004765!1.02e-16!101;UBERON:0001434!1.02e-16!101;UBERON:0001049!6.14e-13!57;UBERON:0005068!6.14e-13!57;UBERON:0006241!6.14e-13!57;UBERON:0007135!6.14e-13!57;UBERON:0000062!1.36e-12!511;UBERON:0003080!1.50e-11!42;UBERON:0002780!5.37e-11!41;UBERON:0001890!5.37e-11!41;UBERON:0006240!5.37e-11!41;UBERON:0000922!3.48e-10!612;UBERON:0002616!1.20e-09!59;UBERON:0000467!1.35e-09!625;UBERON:0000480!1.77e-09!626;UBERON:0002050!2.36e-09!605;UBERON:0005423!2.36e-09!605;UBERON:0000923!3.96e-09!604;UBERON:0005291!3.96e-09!604;UBERON:0006598!3.96e-09!604;UBERON:0002532!3.96e-09!604;UBERON:0000468!4.03e-09!659;UBERON:0002204!7.61e-09!167;UBERON:0002020!7.93e-09!34;UBERON:0003528!7.93e-09!34;UBERON:0003075!9.93e-09!86;UBERON:0007284!9.93e-09!86;UBERON:0001893!1.86e-08!34;UBERON:0002791!2.97e-08!33;UBERON:0002346!4.11e-08!90;UBERON:0001869!9.92e-08!32;UBERON:0000955!1.87e-07!69;UBERON:0006238!1.87e-07!69;UBERON:0001017!2.01e-07!82;UBERON:0003081!2.59e-07!216;UBERON:0005743!4.18e-07!86;UBERON:0000479!6.01e-07!787;UBERON:0002619!8.99e-07!22
|ontology_enrichment_uberon=UBERON:0007023!1.15e-44!115;UBERON:0002390!8.62e-27!102;UBERON:0003061!8.62e-27!102;UBERON:0002193!8.98e-25!112;UBERON:0002371!2.94e-24!80;UBERON:0002405!1.42e-21!115;UBERON:0001474!6.77e-21!86;UBERON:0004765!1.02e-16!101;UBERON:0001434!1.02e-16!101;UBERON:0001049!6.14e-13!57;UBERON:0005068!6.14e-13!57;UBERON:0006241!6.14e-13!57;UBERON:0007135!6.14e-13!57;UBERON:0000062!1.36e-12!511;UBERON:0003080!1.50e-11!42;UBERON:0002780!5.37e-11!41;UBERON:0001890!5.37e-11!41;UBERON:0006240!5.37e-11!41;UBERON:0000922!3.48e-10!612;UBERON:0002616!1.20e-09!59;UBERON:0000467!1.35e-09!625;UBERON:0000480!1.77e-09!626;UBERON:0002050!2.36e-09!605;UBERON:0005423!2.36e-09!605;UBERON:0000923!3.96e-09!604;UBERON:0005291!3.96e-09!604;UBERON:0006598!3.96e-09!604;UBERON:0002532!3.96e-09!604;UBERON:0000468!4.03e-09!659;UBERON:0002204!7.61e-09!167;UBERON:0002020!7.93e-09!34;UBERON:0003528!7.93e-09!34;UBERON:0003075!9.93e-09!86;UBERON:0007284!9.93e-09!86;UBERON:0001893!1.86e-08!34;UBERON:0002791!2.97e-08!33;UBERON:0002346!4.11e-08!90;UBERON:0001869!9.92e-08!32;UBERON:0000955!1.87e-07!69;UBERON:0006238!1.87e-07!69;UBERON:0001017!2.01e-07!82;UBERON:0003081!2.59e-07!216;UBERON:0005743!4.18e-07!86;UBERON:0000479!6.01e-07!787;UBERON:0002619!8.99e-07!22
|tf_chipseq_enrich=SUZ12#23512;5:50.1157809110629:3.15480790456198e-09:2.62956889660454e-07
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}}
}}

Revision as of 12:39, 5 September 2012


Full id: C1988_Macrophage_CD14_Hepatocyte_Monocytederived_liver_migratory_CD14CD16



Phase1 CAGE Peaks

Hg19::chr7:150498348..150498411,-p2@TMEM176B
Hg19::chr7:150498413..150498425,-p6@TMEM176B
Hg19::chr7:150498426..150498465,-p3@TMEM176B
Hg19::chr7:150498588..150498601,+p6@TMEM176A
Hg19::chr7:150498610..150498659,+p4@TMEM176A


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
CD14-positive, CD16-negative classical monocyte1.23e-3342
monopoietic cell4.27e-3363
monocyte4.27e-3363
monoblast4.27e-3363
promonocyte4.27e-3363
macrophage dendritic cell progenitor2.06e-3265
granulocyte monocyte progenitor cell1.70e-3071
myeloid lineage restricted progenitor cell2.95e-3070
myeloid leukocyte4.15e-3076
classical monocyte5.02e-3045
leukocyte2.60e-17140
myeloid cell2.70e-17112
common myeloid progenitor2.70e-17112
nongranular leukocyte1.61e-15119
hematopoietic lineage restricted progenitor cell8.24e-14124
hematopoietic stem cell3.79e-10172
angioblastic mesenchymal cell3.79e-10172
hematopoietic oligopotent progenitor cell4.57e-09165
hematopoietic multipotent progenitor cell4.57e-09165
hematopoietic cell2.56e-08182
intermediate monocyte5.01e-079
CD14-positive, CD16-positive monocyte5.01e-079
Uber Anatomy
Ontology termp-valuen
adult organism1.15e-44115
hematopoietic system8.62e-27102
blood island8.62e-27102
hemolymphoid system8.98e-25112
bone marrow2.94e-2480
immune system1.42e-21115
bone element6.77e-2186
skeletal element1.02e-16101
skeletal system1.02e-16101
neural tube6.14e-1357
neural rod6.14e-1357
future spinal cord6.14e-1357
neural keel6.14e-1357
organ1.36e-12511
anterior neural tube1.50e-1142
regional part of forebrain5.37e-1141
forebrain5.37e-1141
future forebrain5.37e-1141
embryo3.48e-10612
regional part of brain1.20e-0959
anatomical system1.35e-09625
anatomical group1.77e-09626
embryonic structure2.36e-09605
developing anatomical structure2.36e-09605
germ layer3.96e-09604
embryonic tissue3.96e-09604
presumptive structure3.96e-09604
epiblast (generic)3.96e-09604
multi-cellular organism4.03e-09659
musculoskeletal system7.61e-09167
gray matter7.93e-0934
brain grey matter7.93e-0934
neural plate9.93e-0986
presumptive neural plate9.93e-0986
telencephalon1.86e-0834
regional part of telencephalon2.97e-0833
neurectoderm4.11e-0890
cerebral hemisphere9.92e-0832
brain1.87e-0769
future brain1.87e-0769
central nervous system2.01e-0782
lateral plate mesoderm2.59e-07216
tissue6.01e-07787
regional part of cerebral cortex8.99e-0722


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


(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
SUZ12#23512550.11578091106293.15480790456198e-092.62956889660454e-07



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.