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Coexpression cluster:C1988: Difference between revisions

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|full_id=C1988_Macrophage_CD14_Hepatocyte_Monocytederived_liver_migratory_CD14CD16
|full_id=C1988_Macrophage_CD14_Hepatocyte_Monocytederived_liver_migratory_CD14CD16
|id=C1988
|id=C1988
|ontology_enrichment_celltype=CL:0002057!1.23e-33!42;CL:0002194!4.27e-33!63;CL:0000576!4.27e-33!63;CL:0000040!4.27e-33!63;CL:0000559!4.27e-33!63;CL:0002009!2.06e-32!65;CL:0000557!1.70e-30!71;CL:0000839!2.95e-30!70;CL:0000766!4.15e-30!76;CL:0000860!5.02e-30!45;CL:0000738!2.60e-17!140;CL:0000763!2.70e-17!112;CL:0000049!2.70e-17!112;CL:0002087!1.61e-15!119;CL:0002031!8.24e-14!124;CL:0000037!3.79e-10!172;CL:0000566!3.79e-10!172;CL:0002032!4.57e-09!165;CL:0000837!4.57e-09!165;CL:0000988!2.56e-08!182;CL:0002393!5.01e-07!9;CL:0002397!5.01e-07!9
|ontology_enrichment_celltype=CL:0000473!8.24e-54!48;CL:0000234!8.24e-54!48;CL:0002194!4.08e-50!59;CL:0000576!4.08e-50!59;CL:0000040!4.08e-50!59;CL:0000559!4.08e-50!59;CL:0002009!7.82e-48!61;CL:0000860!1.44e-46!42;CL:0002057!1.44e-46!42;CL:0000839!9.77e-43!66;CL:0000557!8.25e-42!67;CL:0000766!1.51e-40!72;CL:0000763!2.46e-25!108;CL:0000049!2.46e-25!108;CL:0000325!1.09e-24!87;CL:0002087!3.42e-22!115;CL:0000738!3.33e-21!136;CL:0002031!1.24e-17!120;CL:0000037!5.66e-14!168;CL:0000566!5.66e-14!168;CL:0002032!1.18e-12!161;CL:0000837!1.18e-12!161;CL:0000988!2.63e-12!177;CL:0000235!1.89e-08!6;CL:0002393!2.59e-08!9;CL:0002397!2.59e-08!9
|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:0002371!1.38e-34!76;UBERON:0002390!3.85e-34!98;UBERON:0003061!3.85e-34!98;UBERON:0002405!6.03e-33!93;UBERON:0002193!1.12e-31!108;UBERON:0001474!1.12e-30!82;UBERON:0007023!4.10e-27!114;UBERON:0004765!2.66e-26!90;UBERON:0001434!7.25e-22!100;UBERON:0003081!1.32e-13!203;UBERON:0000062!5.15e-13!503;UBERON:0002204!1.96e-11!167;UBERON:0002050!1.31e-10!564;UBERON:0000923!1.64e-10!560;UBERON:0010316!1.64e-10!560;UBERON:0005291!1.64e-10!560;UBERON:0006598!1.64e-10!560;UBERON:0010317!1.64e-10!560;UBERON:0002532!1.64e-10!560;UBERON:0005423!4.02e-10!581;UBERON:0000922!5.00e-10!592;UBERON:0000926!2.98e-09!315;UBERON:0004120!2.98e-09!315;UBERON:0006603!2.98e-09!315;UBERON:0000468!8.11e-09!656;UBERON:0000467!2.43e-08!624;UBERON:0000480!2.90e-08!625
|tf_chipseq_enrich=SUZ12#23512;5:50.1157809110629:3.15480790456198e-09:2.62956889660454e-07
|tf_chipseq_enrich=SUZ12#23512;5:50.1157809110629:3.15480790456198e-09:2.62956889660454e-07
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}}
}}

Revision as of 11:55, 19 October 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
defensive cell8.24e-5448
phagocyte8.24e-5448
monopoietic cell4.08e-5059
monocyte4.08e-5059
monoblast4.08e-5059
promonocyte4.08e-5059
macrophage dendritic cell progenitor7.82e-4861
classical monocyte1.44e-4642
CD14-positive, CD16-negative classical monocyte1.44e-4642
myeloid lineage restricted progenitor cell9.77e-4366
granulocyte monocyte progenitor cell8.25e-4267
myeloid leukocyte1.51e-4072
myeloid cell2.46e-25108
common myeloid progenitor2.46e-25108
stuff accumulating cell1.09e-2487
nongranular leukocyte3.42e-22115
leukocyte3.33e-21136
hematopoietic lineage restricted progenitor cell1.24e-17120
hematopoietic stem cell5.66e-14168
angioblastic mesenchymal cell5.66e-14168
hematopoietic oligopotent progenitor cell1.18e-12161
hematopoietic multipotent progenitor cell1.18e-12161
hematopoietic cell2.63e-12177
macrophage1.89e-086
intermediate monocyte2.59e-089
CD14-positive, CD16-positive monocyte2.59e-089
Uber Anatomy
Ontology termp-valuen
bone marrow1.38e-3476
hematopoietic system3.85e-3498
blood island3.85e-3498
immune system6.03e-3393
hemolymphoid system1.12e-31108
bone element1.12e-3082
adult organism4.10e-27114
skeletal element2.66e-2690
skeletal system7.25e-22100
lateral plate mesoderm1.32e-13203
organ5.15e-13503
musculoskeletal system1.96e-11167
embryonic structure1.31e-10564
germ layer1.64e-10560
germ layer / neural crest1.64e-10560
embryonic tissue1.64e-10560
presumptive structure1.64e-10560
germ layer / neural crest derived structure1.64e-10560
epiblast (generic)1.64e-10560
developing anatomical structure4.02e-10581
embryo5.00e-10592
mesoderm2.98e-09315
mesoderm-derived structure2.98e-09315
presumptive mesoderm2.98e-09315
multi-cellular organism8.11e-09656
anatomical system2.43e-08624
anatomical group2.90e-08625


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.