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Coexpression cluster:C4142: Difference between revisions

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|full_id=C4142_trachea_CD14_Whole_immature_Macrophage_Monocytederived_Neutrophils
|full_id=C4142_trachea_CD14_Whole_immature_Macrophage_Monocytederived_Neutrophils
|id=C4142
|id=C4142
|ontology_enrichment_celltype=CL:0000766!5.35e-50!76;CL:0002009!1.27e-47!65;CL:0002194!7.04e-45!63;CL:0000576!7.04e-45!63;CL:0000040!7.04e-45!63;CL:0000559!7.04e-45!63;CL:0000839!3.50e-44!70;CL:0000557!5.44e-44!71;CL:0002057!1.13e-43!42;CL:0000860!6.79e-40!45;CL:0000763!1.80e-39!112;CL:0000049!1.80e-39!112;CL:0000738!3.58e-31!140;CL:0000988!1.28e-25!182;CL:0000037!2.39e-25!172;CL:0000566!2.39e-25!172;CL:0002031!1.43e-24!124;CL:0002032!2.08e-24!165;CL:0000837!2.08e-24!165;CL:0002087!9.57e-24!119;CL:0002393!2.51e-11!9;CL:0002397!2.51e-11!9;CL:0000094!5.35e-09!8;CL:0000990!3.67e-08!8;CL:0000081!5.52e-08!11;CL:0000080!1.92e-07!6;CL:0000840!5.03e-07!5;CL:0001029!5.03e-07!5
|ontology_enrichment_celltype=CL:0002009!7.83e-49!61;CL:0002194!1.59e-47!59;CL:0000576!1.59e-47!59;CL:0000040!1.59e-47!59;CL:0000559!1.59e-47!59;CL:0000557!1.21e-43!67;CL:0000766!1.81e-42!72;CL:0000839!1.51e-41!66;CL:0000473!3.42e-40!48;CL:0000234!3.42e-40!48;CL:0000860!8.12e-37!42;CL:0002057!8.12e-37!42;CL:0000763!2.23e-30!108;CL:0000049!2.23e-30!108;CL:0000738!2.28e-23!136;CL:0002087!2.16e-21!115;CL:0002031!2.81e-20!120;CL:0000325!1.16e-18!87;CL:0002032!4.93e-17!161;CL:0000837!4.93e-17!161;CL:0000037!5.93e-17!168;CL:0000566!5.93e-17!168;CL:0000988!1.42e-15!177;CL:0002393!5.06e-12!9;CL:0002397!5.06e-12!9;CL:0000990!1.24e-10!8;CL:0002619!2.22e-10!3;CL:0000875!8.73e-10!3;CL:0002396!8.73e-10!3;CL:0000451!1.44e-08!10;CL:0000840!7.79e-08!5;CL:0001029!7.79e-08!5
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002390!2.94e-53!102;UBERON:0003061!2.94e-53!102;UBERON:0002193!6.58e-50!112;UBERON:0002371!3.36e-37!80;UBERON:0001474!1.80e-33!86;UBERON:0004765!2.62e-27!101;UBERON:0001434!2.62e-27!101;UBERON:0002405!2.18e-26!115;UBERON:0003081!1.45e-20!216;UBERON:0000178!2.58e-18!15;UBERON:0000179!2.58e-18!15;UBERON:0000463!2.58e-18!15;UBERON:0002204!6.63e-12!167;UBERON:0007023!1.89e-11!115;UBERON:0000926!1.62e-07!448;UBERON:0004120!1.62e-07!448;UBERON:0006603!1.62e-07!448
|ontology_enrichment_uberon=UBERON:0002390!5.55e-49!98;UBERON:0003061!5.55e-49!98;UBERON:0002193!1.85e-45!108;UBERON:0002371!2.19e-37!76;UBERON:0001474!5.69e-34!82;UBERON:0002405!1.63e-32!93;UBERON:0004765!3.99e-30!90;UBERON:0001434!3.50e-26!100;UBERON:0003081!9.69e-20!203;UBERON:0000178!6.73e-15!15;UBERON:0000179!6.73e-15!15;UBERON:0000463!6.73e-15!15;UBERON:0002204!6.09e-13!167;UBERON:0000926!3.27e-11!315;UBERON:0004120!3.27e-11!315;UBERON:0006603!3.27e-11!315;UBERON:0003127!5.67e-07!2;UBERON:0000341!6.75e-07!2
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}}
}}

Revision as of 15:42, 19 October 2012


Full id: C4142_trachea_CD14_Whole_immature_Macrophage_Monocytederived_Neutrophils



Phase1 CAGE Peaks

Hg19::chr2:169923504..169923517,+p12@DHRS9
Hg19::chr2:169923651..169923667,+p7@DHRS9
Hg19::chr2:169923690..169923703,+p8@DHRS9


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
macrophage dendritic cell progenitor7.83e-4961
monopoietic cell1.59e-4759
monocyte1.59e-4759
monoblast1.59e-4759
promonocyte1.59e-4759
granulocyte monocyte progenitor cell1.21e-4367
myeloid leukocyte1.81e-4272
myeloid lineage restricted progenitor cell1.51e-4166
defensive cell3.42e-4048
phagocyte3.42e-4048
classical monocyte8.12e-3742
CD14-positive, CD16-negative classical monocyte8.12e-3742
myeloid cell2.23e-30108
common myeloid progenitor2.23e-30108
leukocyte2.28e-23136
nongranular leukocyte2.16e-21115
hematopoietic lineage restricted progenitor cell2.81e-20120
stuff accumulating cell1.16e-1887
hematopoietic oligopotent progenitor cell4.93e-17161
hematopoietic multipotent progenitor cell4.93e-17161
hematopoietic stem cell5.93e-17168
angioblastic mesenchymal cell5.93e-17168
hematopoietic cell1.42e-15177
intermediate monocyte5.06e-129
CD14-positive, CD16-positive monocyte5.06e-129
conventional dendritic cell1.24e-108
adult endothelial progenitor cell2.22e-103
non-classical monocyte8.73e-103
CD14-low, CD16-positive monocyte8.73e-103
dendritic cell1.44e-0810
immature conventional dendritic cell7.79e-085
common dendritic progenitor7.79e-085
Uber Anatomy
Ontology termp-valuen
hematopoietic system5.55e-4998
blood island5.55e-4998
hemolymphoid system1.85e-45108
bone marrow2.19e-3776
bone element5.69e-3482
immune system1.63e-3293
skeletal element3.99e-3090
skeletal system3.50e-26100
lateral plate mesoderm9.69e-20203
blood6.73e-1515
haemolymphatic fluid6.73e-1515
organism substance6.73e-1515
musculoskeletal system6.09e-13167
mesoderm3.27e-11315
mesoderm-derived structure3.27e-11315
presumptive mesoderm3.27e-11315
open tracheal system trachea5.67e-072
throat6.75e-072


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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