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Coexpression cluster:C2568: Difference between revisions

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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C2568_CD4_Smooth_Aortic_acute_CD34_Fibroblast_CD8
|full_id=C2568_CD4_Smooth_Aortic_acute_CD34_Fibroblast_CD8
|gostat_on_coexpression_clusters=GO:0005842!cytosolic large ribosomal subunit (sensu Eukaryota)!5.52188315379147e-05!6164;6130$GO:0005830!cytosolic ribosome (sensu Eukaryota)!0.000103395585369577!6164;6130$GO:0015934!large ribosomal subunit!0.000135625200268563!6164;6130$GO:0044445!cytosolic part!0.000334498691046984!6164;6130$GO:0033279!ribosomal subunit!0.000372239011198639!6164;6130$GO:0042788!polysomal ribosome!0.00168758983169338!6130$GO:0005829!cytosol!0.00171424291592199!6164;6130$GO:0003735!structural constituent of ribosome!0.00253119844918806!6164;6130$GO:0005844!polysome!0.00253119844918806!6130$GO:0005840!ribosome!0.00268251742263055!6164;6130$GO:0003723!RNA binding!0.00322991211205015!6164;6130$GO:0030529!ribonucleoprotein complex!0.00401754259108733!6164;6130$GO:0006412!translation!0.0041720570111862!6164;6130$GO:0009059!macromolecule biosynthetic process!0.00650588975790638!6164;6130$GO:0044249!cellular biosynthetic process!0.00932462001903585!6164;6130$GO:0009058!biosynthetic process!0.0140181638787613!6164;6130$GO:0042254!ribosome biogenesis and assembly!0.0165024219924451!6130$GO:0043232!intracellular non-membrane-bound organelle!0.016714845025811!6164;6130$GO:0043228!non-membrane-bound organelle!0.016714845025811!6164;6130$GO:0032991!macromolecular complex!0.0276252430289505!6164;6130$GO:0022613!ribonucleoprotein complex biogenesis and assembly!0.0276252430289505!6130$GO:0044446!intracellular organelle part!0.0276252430289505!6164;6130$GO:0044422!organelle part!0.0276252430289505!6164;6130$GO:0044444!cytoplasmic part!0.0327293167586561!6164;6130$GO:0010467!gene expression!0.0441384679540688!6164;6130$GO:0044267!cellular protein metabolic process!0.0441384679540688!6164;6130$GO:0044260!cellular macromolecule metabolic process!0.0441384679540688!6164;6130$GO:0019538!protein metabolic process!0.0456568104643413!6164;6130
|gostat_on_coexpression_clusters=GO:0005842!cytosolic large ribosomal subunit (sensu Eukaryota)!5.52188315379147e-05!6164;6130$GO:0005830!cytosolic ribosome (sensu Eukaryota)!0.000103395585369577!6164;6130$GO:0015934!large ribosomal subunit!0.000135625200268563!6164;6130$GO:0044445!cytosolic part!0.000334498691046984!6164;6130$GO:0033279!ribosomal subunit!0.000372239011198639!6164;6130$GO:0042788!polysomal ribosome!0.00168758983169338!6130$GO:0005829!cytosol!0.00171424291592199!6164;6130$GO:0003735!structural constituent of ribosome!0.00253119844918806!6164;6130$GO:0005844!polysome!0.00253119844918806!6130$GO:0005840!ribosome!0.00268251742263055!6164;6130$GO:0003723!RNA binding!0.00322991211205015!6164;6130$GO:0030529!ribonucleoprotein complex!0.00401754259108733!6164;6130$GO:0006412!translation!0.0041720570111862!6164;6130$GO:0009059!macromolecule biosynthetic process!0.00650588975790638!6164;6130$GO:0044249!cellular biosynthetic process!0.00932462001903585!6164;6130$GO:0009058!biosynthetic process!0.0140181638787613!6164;6130$GO:0042254!ribosome biogenesis and assembly!0.0165024219924451!6130$GO:0043232!intracellular non-membrane-bound organelle!0.016714845025811!6164;6130$GO:0043228!non-membrane-bound organelle!0.016714845025811!6164;6130$GO:0032991!macromolecular complex!0.0276252430289505!6164;6130$GO:0022613!ribonucleoprotein complex biogenesis and assembly!0.0276252430289505!6130$GO:0044446!intracellular organelle part!0.0276252430289505!6164;6130$GO:0044422!organelle part!0.0276252430289505!6164;6130$GO:0044444!cytoplasmic part!0.0327293167586561!6164;6130$GO:0010467!gene expression!0.0441384679540688!6164;6130$GO:0044267!cellular protein metabolic process!0.0441384679540688!6164;6130$GO:0044260!cellular macromolecule metabolic process!0.0441384679540688!6164;6130$GO:0019538!protein metabolic process!0.0456568104643413!6164;6130

Revision as of 15:19, 12 September 2012


Full id: C2568_CD4_Smooth_Aortic_acute_CD34_Fibroblast_CD8



Phase1 CAGE Peaks

Hg19::chr1:22234543..22234549,+p1@ENST00000423231
Hg19::chr1:53238346..53238348,-p1@ENST00000437890
Hg19::chr4:109541723..109541738,+p1@RPL34
Hg19::chr9:136215044..136215086,+p1@RPL7A


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


p.valueFDRnGenesnPathwayName
1.02743394677841e-050.00315487951907255292Ribosome (KEGG):03010
1.05001491264167e-050.00315487951907255293Cytoplasmic Ribosomal Proteins (Wikipathways):WP477
0.0001071614097380440.01076825531843682296Metabolism of proteins (Reactome):REACT_17015
1.58091305570944e-050.003154879519072552114Regulation of beta-cell development (Reactome):REACT_13698
0.0002169981730403220.01716998044181552421Gene Expression (Reactome):REACT_71
0.0001190802325893480.01076825531843682312Diabetes pathways (Reactome):REACT_15380
2.49200593923582e-050.003154879519072552143Influenza Infection (Reactome):REACT_6167
2.32019424245013e-050.003154879519072552138{RPS27A,138} (Static Module):NA



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:0005842cytosolic large ribosomal subunit (sensu Eukaryota)5.52188315379147e-05
GO:0005830cytosolic ribosome (sensu Eukaryota)0.000103395585369577
GO:0015934large ribosomal subunit0.000135625200268563
GO:0044445cytosolic part0.000334498691046984
GO:0033279ribosomal subunit0.000372239011198639
GO:0042788polysomal ribosome0.00168758983169338
GO:0005829cytosol0.00171424291592199
GO:0003735structural constituent of ribosome0.00253119844918806
GO:0005844polysome0.00253119844918806
GO:0005840ribosome0.00268251742263055
GO:0003723RNA binding0.00322991211205015
GO:0030529ribonucleoprotein complex0.00401754259108733
GO:0006412translation0.0041720570111862
GO:0009059macromolecule biosynthetic process0.00650588975790638
GO:0044249cellular biosynthetic process0.00932462001903585
GO:0009058biosynthetic process0.0140181638787613
GO:0042254ribosome biogenesis and assembly0.0165024219924451
GO:0043232intracellular non-membrane-bound organelle0.016714845025811
GO:0043228non-membrane-bound organelle0.016714845025811
GO:0032991macromolecular complex0.0276252430289505
GO:0022613ribonucleoprotein complex biogenesis and assembly0.0276252430289505
GO:0044446intracellular organelle part0.0276252430289505
GO:0044422organelle part0.0276252430289505
GO:0044444cytoplasmic part0.0327293167586561
GO:0010467gene expression0.0441384679540688
GO:0044267cellular protein metabolic process0.0441384679540688
GO:0044260cellular macromolecule metabolic process0.0441384679540688
GO:0019538protein metabolic process0.0456568104643413



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
native cell2.47e-24722
hematopoietic cell2.64e-19182
hematopoietic lineage restricted progenitor cell4.25e-19124
somatic cell1.39e-18591
hematopoietic stem cell2.01e-18172
angioblastic mesenchymal cell2.01e-18172
stem cell3.89e-18444
CD14-positive, CD16-negative classical monocyte4.11e-1842
nongranular leukocyte8.13e-18119
multi fate stem cell9.24e-18430
hematopoietic oligopotent progenitor cell1.88e-17165
hematopoietic multipotent progenitor cell1.88e-17165
somatic stem cell5.00e-17436
animal cell9.81e-17679
eukaryotic cell9.81e-17679
connective tissue cell1.01e-16365
leukocyte2.92e-16140
classical monocyte8.69e-1645
mesenchymal cell2.67e-15358
motile cell3.50e-13390
lymphoid lineage restricted progenitor cell4.92e-1152
lymphocyte1.04e-1053
common lymphoid progenitor1.04e-1053
macrophage dendritic cell progenitor1.03e-0865
myeloid lineage restricted progenitor cell3.11e-0870
mature alpha-beta T cell3.16e-0818
alpha-beta T cell3.16e-0818
immature T cell3.16e-0818
mature T cell3.16e-0818
immature alpha-beta T cell3.16e-0818
myeloid cell4.83e-08112
common myeloid progenitor4.83e-08112
monopoietic cell4.90e-0863
monocyte4.90e-0863
monoblast4.90e-0863
promonocyte4.90e-0863
granulocyte monocyte progenitor cell5.50e-0871
B cell1.48e-0714
T cell4.41e-0725
pro-T cell4.41e-0725
Uber Anatomy
Ontology termp-valuen
connective tissue2.30e-16375
bone marrow4.89e-0980
hemolymphoid system3.00e-08112
hematopoietic system3.69e-08102
blood island3.69e-08102
bone element4.14e-0886
skeletal element6.02e-07101
skeletal system6.02e-07101


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
BRCA1#672210.09211532161190.0137713969900260.0484739621260263
KAT2A#26481154.02250.006476819949311040.0281249261438649
ZZZ3#260092119.7066062176170.0001039630683859570.00145254834771385



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.