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Coexpression cluster:C1308: Difference between revisions

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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C1308_CD14_CD4_Basophils_Peripheral_Neutrophils_Eosinophils_CD8
|full_id=C1308_CD14_CD4_Basophils_Peripheral_Neutrophils_Eosinophils_CD8
|gostat_on_coexpression_clusters=GO:0004221!ubiquitin thiolesterase activity!0.0316849169904627!9960$GO:0004843!ubiquitin-specific protease activity!0.0316849169904627!9960$GO:0019783!small conjugating protein-specific protease activity!0.0316849169904627!9960$GO:0016790!thiolester hydrolase activity!0.0316849169904627!9960$GO:0006511!ubiquitin-dependent protein catabolic process!0.0316849169904627!9960$GO:0043632!modification-dependent macromolecule catabolic process!0.0316849169904627!9960$GO:0019941!modification-dependent protein catabolic process!0.0316849169904627!9960$GO:0051603!proteolysis involved in cellular protein catabolic process!0.0316849169904627!9960$GO:0044257!cellular protein catabolic process!0.0316849169904627!9960$GO:0008234!cysteine-type peptidase activity!0.0316849169904627!9960$GO:0030163!protein catabolic process!0.0342956231334896!9960$GO:0043285!biopolymer catabolic process!0.0400918403391028!9960$GO:0044265!cellular macromolecule catabolic process!0.0415552303577736!9960$GO:0006512!ubiquitin cycle!0.0415552303577736!9960$GO:0009057!macromolecule catabolic process!0.0441540091840339!9960
|gostat_on_coexpression_clusters=GO:0004221!ubiquitin thiolesterase activity!0.0316849169904627!9960$GO:0004843!ubiquitin-specific protease activity!0.0316849169904627!9960$GO:0019783!small conjugating protein-specific protease activity!0.0316849169904627!9960$GO:0016790!thiolester hydrolase activity!0.0316849169904627!9960$GO:0006511!ubiquitin-dependent protein catabolic process!0.0316849169904627!9960$GO:0043632!modification-dependent macromolecule catabolic process!0.0316849169904627!9960$GO:0019941!modification-dependent protein catabolic process!0.0316849169904627!9960$GO:0051603!proteolysis involved in cellular protein catabolic process!0.0316849169904627!9960$GO:0044257!cellular protein catabolic process!0.0316849169904627!9960$GO:0008234!cysteine-type peptidase activity!0.0316849169904627!9960$GO:0030163!protein catabolic process!0.0342956231334896!9960$GO:0043285!biopolymer catabolic process!0.0400918403391028!9960$GO:0044265!cellular macromolecule catabolic process!0.0415552303577736!9960$GO:0006512!ubiquitin cycle!0.0415552303577736!9960$GO:0009057!macromolecule catabolic process!0.0441540091840339!9960

Revision as of 13:49, 12 September 2012


Full id: C1308_CD14_CD4_Basophils_Peripheral_Neutrophils_Eosinophils_CD8



Phase1 CAGE Peaks

Hg19::chr10:23727926..23727957,+p4@OTUD1
Hg19::chr10:23727989..23728040,+p2@OTUD1
Hg19::chr10:23728041..23728084,+p3@OTUD1
Hg19::chr15:63796779..63796863,+p1@USP3
Hg19::chr15:63796867..63796887,+p2@USP3
Hg19::chr15:63796904..63796916,+p4@USP3


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

GO IDGO nameFDR corrected p-value
GO:0004221ubiquitin thiolesterase activity0.0316849169904627
GO:0004843ubiquitin-specific protease activity0.0316849169904627
GO:0019783small conjugating protein-specific protease activity0.0316849169904627
GO:0016790thiolester hydrolase activity0.0316849169904627
GO:0006511ubiquitin-dependent protein catabolic process0.0316849169904627
GO:0043632modification-dependent macromolecule catabolic process0.0316849169904627
GO:0019941modification-dependent protein catabolic process0.0316849169904627
GO:0051603proteolysis involved in cellular protein catabolic process0.0316849169904627
GO:0044257cellular protein catabolic process0.0316849169904627
GO:0008234cysteine-type peptidase activity0.0316849169904627
GO:0030163protein catabolic process0.0342956231334896
GO:0043285biopolymer catabolic process0.0400918403391028
GO:0044265cellular macromolecule catabolic process0.0415552303577736
GO:0006512ubiquitin cycle0.0415552303577736
GO:0009057macromolecule catabolic process0.0441540091840339



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
leukocyte1.10e-39140
hematopoietic lineage restricted progenitor cell3.21e-32124
nongranular leukocyte6.21e-32119
myeloid leukocyte2.55e-3076
CD14-positive, CD16-negative classical monocyte7.82e-2742
granulocyte monocyte progenitor cell1.15e-2671
classical monocyte5.60e-2645
hematopoietic stem cell2.85e-25172
angioblastic mesenchymal cell2.85e-25172
macrophage dendritic cell progenitor3.03e-2565
myeloid lineage restricted progenitor cell1.96e-2470
monopoietic cell2.39e-2463
monocyte2.39e-2463
monoblast2.39e-2463
promonocyte2.39e-2463
hematopoietic oligopotent progenitor cell2.46e-23165
hematopoietic multipotent progenitor cell2.46e-23165
hematopoietic cell2.72e-21182
myeloid cell1.31e-15112
common myeloid progenitor1.31e-15112
mature alpha-beta T cell7.56e-0918
alpha-beta T cell7.56e-0918
immature T cell7.56e-0918
mature T cell7.56e-0918
immature alpha-beta T cell7.56e-0918
lymphoid lineage restricted progenitor cell4.97e-0852
lymphocyte1.37e-0753
common lymphoid progenitor1.37e-0753
intermediate monocyte9.66e-079
CD14-positive, CD16-positive monocyte9.66e-079
Uber Anatomy
Ontology termp-valuen
hematopoietic system2.83e-25102
blood island2.83e-25102
hemolymphoid system1.49e-23112
bone marrow9.04e-2180
bone element3.92e-1986
immune system9.24e-16115
skeletal element3.85e-13101
skeletal system3.85e-13101
adult organism2.08e-07115


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
ATF3#467311.23158726300440.001593459971184230.010038567132978
BCL11A#53335314.18472755180350.0008080831849424810.00616790175781684
BCLAF1#9774310.82632380506090.001772351046991060.0108871056932537
BHLHE40#8553322.43590677348870.0002103196104780280.00244605454328672
CCNT2#90566.336201576962631.54467812014647e-050.000362283041073383
CTCF#1066465.360256373075034.21437267579784e-050.000754706563593365
E2F4#1874612.66806031528442.41728555395527e-071.26736388538923e-05
E2F6#187665.017155731697396.26776799983417e-050.00102425195139208
EGR1#195864.988179094810146.48943962979974e-050.0010543724105424
ELF1#199764.258097958807540.0001677224776288830.00205066352623307
ELK4#200538.117840829234010.004056113134185760.019405240477381
FOSL2#235538.465100302280850.003598315634615090.0182181736747899
FOXA1#3169611.08141974938555.39600313513231e-072.50245635626147e-05
FOXA2#3170312.31523187633260.001219712440124520.0082041313540391
GTF2B#2959315.97191496716210.0005711653715892990.00486636810600545
GTF2F1#296236.369830438378830.008068208196303160.03191076254691
HDAC2#3066613.41562023662631.71355402088576e-079.4190457045941e-06
HEY1#2346264.040111043105710.0002298968555807510.00252872013691396
HMGN3#932468.178547723350593.33956428934731e-060.000111467163571474
HNF4A#3172311.56614518147680.001463487150085730.00937527660355786
HNF4G#3174314.37671126322340.0007769772937197380.00608889709452958
IRF1#365967.63716375356395.03701715640675e-060.000155455388533677
IRF4#3662310.95725634337210.001711753441810940.0106877394457639
JUN#372536.256414596168170.008486346850954870.0324048692467141
MAX#414966.452555509007121.3848964723355e-050.000334266703661307
MEF2A#420539.371615454822030.002687399947103910.0147969929921755
MEF2C#4208320.6556772463120.0002683563494060410.0028654400138654
MXI1#460169.96157162875931.02262624227062e-064.2978697028773e-05
MYC#460965.22228187160944.92821127172503e-050.00085313684237973
NR3C1#290837.486511665586520.00510866965984070.0237553139182593
POLR2A#543062.147453176558070.01019570676818780.0379821444324154
RFX5#599336.023955413597550.009437904036335060.0355997276672492
RXRA#6256310.03730856956660.002205419116789220.0127037541855578
SIN3A#2594265.408884726815143.99207083571449e-050.000741864565856202
SMC3#9126615.04493284493288.61317699636729e-085.12565009870999e-06
SRF#672236.89858913108390.00644245168930370.0279966384545911
STAT1#6772310.35329374859960.002016680459920930.0117199983614536
TAF1#687263.343046285745290.0007162474284635620.00572422445525758
TCF12#693835.317232451093210.013367345733860.0472364141802944
TCF7L2#6934610.77017656313736.40204410218762e-072.90832137446008e-05
USF1#739166.361499277207961.50818327938273e-050.000356849011136052
USF2#739236.49609869253480.007634319815300560.0314524941692377
ZEB1#693538.444216008771930.003623843810733590.0183332020804691
ZNF263#1012768.221841637010683.23542093046082e-060.000108615919818836



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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