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Coexpression cluster:C1766: Difference between revisions

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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C1766_CD14_CD14CD16_Hair_CD8_CD19_xeroderma_CD4
|full_id=C1766_CD14_CD14CD16_Hair_CD8_CD19_xeroderma_CD4
|gostat_on_coexpression_clusters=GO:0004298!threonine endopeptidase activity!4.45890006046998e-07!5696;5699;5698$GO:0005839!proteasome core complex (sensu Eukaryota)!4.45890006046998e-07!5696;5699;5698$GO:0000502!proteasome complex (sensu Eukaryota)!1.67734810946468e-06!5696;5699;5698$GO:0005829!cytosol!2.45545651619859e-06!5696;5699;5698;6891$GO:0006955!immune response!3.17272568259787e-05!5696;5699;5698;6891$GO:0006511!ubiquitin-dependent protein catabolic process!3.17272568259787e-05!5696;5699;5698$GO:0043632!modification-dependent macromolecule catabolic process!3.17272568259787e-05!5696;5699;5698$GO:0019941!modification-dependent protein catabolic process!3.17272568259787e-05!5696;5699;5698$GO:0051603!proteolysis involved in cellular protein catabolic process!3.17272568259787e-05!5696;5699;5698$GO:0044257!cellular protein catabolic process!3.17272568259787e-05!5696;5699;5698$GO:0002376!immune system process!3.18547758936163e-05!5696;5699;5698;6891$GO:0030163!protein catabolic process!4.79337041589452e-05!5696;5699;5698$GO:0043285!biopolymer catabolic process!9.17363901730058e-05!5696;5699;5698$GO:0044265!cellular macromolecule catabolic process!0.000130138439451392!5696;5699;5698$GO:0009057!macromolecule catabolic process!0.000207011545222337!5696;5699;5698$GO:0004175!endopeptidase activity!0.000372993694047045!5696;5699;5698$GO:0043234!protein complex!0.000372993694047045!5696;5699;5698;6891$GO:0044248!cellular catabolic process!0.000372993694047045!5696;5699;5698$GO:0009056!catabolic process!0.000612888261624961!5696;5699;5698$GO:0004409!homoaconitate hydratase activity!0.000747674555516307!6891$GO:0032991!macromolecular complex!0.00103080130692212!5696;5699;5698;6891$GO:0016787!hydrolase activity!0.00103483066727459!5696;5699;5698;6891$GO:0008233!peptidase activity!0.00103483066727459!5696;5699;5698$GO:0006508!proteolysis!0.00119483757108028!5696;5699;5698$GO:0046967!cytosol to ER transport!0.00119622646674452!6891$GO:0044444!cytoplasmic part!0.00149521705842028!5696;5699;5698;6891$GO:0015440!peptide-transporting ATPase activity!0.00149521705842028!6891$GO:0042825!TAP complex!0.00149521705842028!6891$GO:0046980!tapasin binding!0.00149521705842028!6891$GO:0015433!peptide antigen-transporting ATPase activity!0.00149521705842028!6891$GO:0046978!TAP1 binding!0.00175900121882525!6891$GO:0046977!TAP binding!0.00175900121882525!6891$GO:0042824!MHC class I peptide loading complex!0.00175900121882525!6891$GO:0046979!TAP2 binding!0.00175900121882525!6891$GO:0042301!phosphate binding!0.00249169833156373!6891$GO:0015198!oligopeptide transporter activity!0.00249169833156373!6891$GO:0019538!protein metabolic process!0.00303212289754489!5696;5699;5698;6891$GO:0015197!peptide transporter activity!0.00314713046787477!6891$GO:0042288!MHC class I protein binding!0.00344958683718131!6891$GO:0002483!antigen processing and presentation of endogenous peptide antigen!0.00583164475744578!6891$GO:0019885!antigen processing and presentation of endogenous peptide antigen via MHC class I!0.00583164475744578!6891$GO:0006857!oligopeptide transport!0.00604832873003494!6891$GO:0042605!peptide antigen binding!0.00611274679452986!6891$GO:0019883!antigen processing and presentation of endogenous antigen!0.00611274679452986!6891$GO:0005737!cytoplasm!0.00663599333603718!5696;5699;5698;6891$GO:0042287!MHC protein binding!0.00746948551180881!6891$GO:0043231!intracellular membrane-bound organelle!0.011881802746805!5696;5699;5698;6891$GO:0043227!membrane-bound organelle!0.011881802746805!5696;5699;5698;6891$GO:0015833!peptide transport!0.011881802746805!6891$GO:0005788!endoplasmic reticulum lumen!0.0190872887198677!6891$GO:0006959!humoral immune response!0.0219186774220755!5699$GO:0043229!intracellular organelle!0.0241778826458626!5696;5699;5698;6891$GO:0043226!organelle!0.0241778826458626!5696;5699;5698;6891$GO:0016836!hydro-lyase activity!0.0248247132780344!6891$GO:0043170!macromolecule metabolic process!0.0264901850198828!5696;5699;5698;6891$GO:0016835!carbon-oxygen lyase activity!0.0264901850198828!6891$GO:0002474!antigen processing and presentation of peptide antigen via MHC class I!0.0264901850198828!6891$GO:0046982!protein heterodimerization activity!0.0264901850198828!6891$GO:0048002!antigen processing and presentation of peptide antigen!0.0264901850198828!6891$GO:0044267!cellular protein metabolic process!0.0329518394413252!5696;5699;5698$GO:0044260!cellular macromolecule metabolic process!0.0336207880593579!5696;5699;5698$GO:0042803!protein homodimerization activity!0.03784391734532!6891$GO:0005634!nucleus!0.0395329301440715!5696;5699;5698$GO:0044238!primary metabolic process!0.0395329301440715!5696;5699;5698;6891$GO:0003823!antigen binding!0.0404041470685052!6891$GO:0044424!intracellular part!0.040719536022715!5696;5699;5698;6891$GO:0042277!peptide binding!0.0460001800729374!6891
|gostat_on_coexpression_clusters=GO:0004298!threonine endopeptidase activity!4.45890006046998e-07!5696;5699;5698$GO:0005839!proteasome core complex (sensu Eukaryota)!4.45890006046998e-07!5696;5699;5698$GO:0000502!proteasome complex (sensu Eukaryota)!1.67734810946468e-06!5696;5699;5698$GO:0005829!cytosol!2.45545651619859e-06!5696;5699;5698;6891$GO:0006955!immune response!3.17272568259787e-05!5696;5699;5698;6891$GO:0006511!ubiquitin-dependent protein catabolic process!3.17272568259787e-05!5696;5699;5698$GO:0043632!modification-dependent macromolecule catabolic process!3.17272568259787e-05!5696;5699;5698$GO:0019941!modification-dependent protein catabolic process!3.17272568259787e-05!5696;5699;5698$GO:0051603!proteolysis involved in cellular protein catabolic process!3.17272568259787e-05!5696;5699;5698$GO:0044257!cellular protein catabolic process!3.17272568259787e-05!5696;5699;5698$GO:0002376!immune system process!3.18547758936163e-05!5696;5699;5698;6891$GO:0030163!protein catabolic process!4.79337041589452e-05!5696;5699;5698$GO:0043285!biopolymer catabolic process!9.17363901730058e-05!5696;5699;5698$GO:0044265!cellular macromolecule catabolic process!0.000130138439451392!5696;5699;5698$GO:0009057!macromolecule catabolic process!0.000207011545222337!5696;5699;5698$GO:0004175!endopeptidase activity!0.000372993694047045!5696;5699;5698$GO:0043234!protein complex!0.000372993694047045!5696;5699;5698;6891$GO:0044248!cellular catabolic process!0.000372993694047045!5696;5699;5698$GO:0009056!catabolic process!0.000612888261624961!5696;5699;5698$GO:0004409!homoaconitate hydratase activity!0.000747674555516307!6891$GO:0032991!macromolecular complex!0.00103080130692212!5696;5699;5698;6891$GO:0016787!hydrolase activity!0.00103483066727459!5696;5699;5698;6891$GO:0008233!peptidase activity!0.00103483066727459!5696;5699;5698$GO:0006508!proteolysis!0.00119483757108028!5696;5699;5698$GO:0046967!cytosol to ER transport!0.00119622646674452!6891$GO:0044444!cytoplasmic part!0.00149521705842028!5696;5699;5698;6891$GO:0015440!peptide-transporting ATPase activity!0.00149521705842028!6891$GO:0042825!TAP complex!0.00149521705842028!6891$GO:0046980!tapasin binding!0.00149521705842028!6891$GO:0015433!peptide antigen-transporting ATPase activity!0.00149521705842028!6891$GO:0046978!TAP1 binding!0.00175900121882525!6891$GO:0046977!TAP binding!0.00175900121882525!6891$GO:0042824!MHC class I peptide loading complex!0.00175900121882525!6891$GO:0046979!TAP2 binding!0.00175900121882525!6891$GO:0042301!phosphate binding!0.00249169833156373!6891$GO:0015198!oligopeptide transporter activity!0.00249169833156373!6891$GO:0019538!protein metabolic process!0.00303212289754489!5696;5699;5698;6891$GO:0015197!peptide transporter activity!0.00314713046787477!6891$GO:0042288!MHC class I protein binding!0.00344958683718131!6891$GO:0002483!antigen processing and presentation of endogenous peptide antigen!0.00583164475744578!6891$GO:0019885!antigen processing and presentation of endogenous peptide antigen via MHC class I!0.00583164475744578!6891$GO:0006857!oligopeptide transport!0.00604832873003494!6891$GO:0042605!peptide antigen binding!0.00611274679452986!6891$GO:0019883!antigen processing and presentation of endogenous antigen!0.00611274679452986!6891$GO:0005737!cytoplasm!0.00663599333603718!5696;5699;5698;6891$GO:0042287!MHC protein binding!0.00746948551180881!6891$GO:0043231!intracellular membrane-bound organelle!0.011881802746805!5696;5699;5698;6891$GO:0043227!membrane-bound organelle!0.011881802746805!5696;5699;5698;6891$GO:0015833!peptide transport!0.011881802746805!6891$GO:0005788!endoplasmic reticulum lumen!0.0190872887198677!6891$GO:0006959!humoral immune response!0.0219186774220755!5699$GO:0043229!intracellular organelle!0.0241778826458626!5696;5699;5698;6891$GO:0043226!organelle!0.0241778826458626!5696;5699;5698;6891$GO:0016836!hydro-lyase activity!0.0248247132780344!6891$GO:0043170!macromolecule metabolic process!0.0264901850198828!5696;5699;5698;6891$GO:0016835!carbon-oxygen lyase activity!0.0264901850198828!6891$GO:0002474!antigen processing and presentation of peptide antigen via MHC class I!0.0264901850198828!6891$GO:0046982!protein heterodimerization activity!0.0264901850198828!6891$GO:0048002!antigen processing and presentation of peptide antigen!0.0264901850198828!6891$GO:0044267!cellular protein metabolic process!0.0329518394413252!5696;5699;5698$GO:0044260!cellular macromolecule metabolic process!0.0336207880593579!5696;5699;5698$GO:0042803!protein homodimerization activity!0.03784391734532!6891$GO:0005634!nucleus!0.0395329301440715!5696;5699;5698$GO:0044238!primary metabolic process!0.0395329301440715!5696;5699;5698;6891$GO:0003823!antigen binding!0.0404041470685052!6891$GO:0044424!intracellular part!0.040719536022715!5696;5699;5698;6891$GO:0042277!peptide binding!0.0460001800729374!6891

Revision as of 14:22, 12 September 2012


Full id: C1766_CD14_CD14CD16_Hair_CD8_CD19_xeroderma_CD4



Phase1 CAGE Peaks

Hg19::chr16:67970711..67970770,-p1@PSMB10
Hg19::chr6:32806506..32806579,-p1@TAP2
Hg19::chr6:32811771..32811831,-p1@PSMB8
Hg19::chr6:32821924..32821931,+p3@PSMB9
Hg19::chr6:32821956..32821975,+p1@PSMB9


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
1.46259452862696e-089.05665559813991e-06345Proteasome (KEGG):03050
4.292253837981e-089.05665559813991e-06364Proteasome Degradation (Wikipathways):WP183
2.67613900622899e-074.23498997735737e-053117Cell Cycle Checkpoints (Reactome):REACT_1538
1.34823063570187e-069.48255547110314e-053200DNA Replication (Reactome):REACT_383
5.28055171391627e-060.00033425892349093315Cell Cycle, Mitotic (Reactome):REACT_152
7.41609277987709e-077.82397788277033e-053164Metabolism of RNA (Reactome):REACT_21257
4.292253837981e-089.05665559813991e-06364Signaling by Wnt (Reactome):REACT_11045
5.33165031389329e-076.7498692973889e-053147Apoptosis (Reactome):REACT_578
1.23011302483476e-069.48255547110314e-053194HIV Infection (Reactome):REACT_6185
1.24930054759413e-069.48255547110314e-053195Metabolism of amino acids and derivatives (Reactome):REACT_13
6.99828407380497e-060.0004027194380653223346{CDC2,351} (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:0004298threonine endopeptidase activity4.45890006046998e-07
GO:0005839proteasome core complex (sensu Eukaryota)4.45890006046998e-07
GO:0000502proteasome complex (sensu Eukaryota)1.67734810946468e-06
GO:0005829cytosol2.45545651619859e-06
GO:0006955immune response3.17272568259787e-05
GO:0006511ubiquitin-dependent protein catabolic process3.17272568259787e-05
GO:0043632modification-dependent macromolecule catabolic process3.17272568259787e-05
GO:0019941modification-dependent protein catabolic process3.17272568259787e-05
GO:0051603proteolysis involved in cellular protein catabolic process3.17272568259787e-05
GO:0044257cellular protein catabolic process3.17272568259787e-05
GO:0002376immune system process3.18547758936163e-05
GO:0030163protein catabolic process4.79337041589452e-05
GO:0043285biopolymer catabolic process9.17363901730058e-05
GO:0044265cellular macromolecule catabolic process0.000130138439451392
GO:0009057macromolecule catabolic process0.000207011545222337
GO:0004175endopeptidase activity0.000372993694047045
GO:0043234protein complex0.000372993694047045
GO:0044248cellular catabolic process0.000372993694047045
GO:0009056catabolic process0.000612888261624961
GO:0004409homoaconitate hydratase activity0.000747674555516307
GO:0032991macromolecular complex0.00103080130692212
GO:0016787hydrolase activity0.00103483066727459
GO:0008233peptidase activity0.00103483066727459
GO:0006508proteolysis0.00119483757108028
GO:0046967cytosol to ER transport0.00119622646674452
GO:0044444cytoplasmic part0.00149521705842028
GO:0015440peptide-transporting ATPase activity0.00149521705842028
GO:0042825TAP complex0.00149521705842028
GO:0046980tapasin binding0.00149521705842028
GO:0015433peptide antigen-transporting ATPase activity0.00149521705842028
GO:0046978TAP1 binding0.00175900121882525
GO:0046977TAP binding0.00175900121882525
GO:0042824MHC class I peptide loading complex0.00175900121882525
GO:0046979TAP2 binding0.00175900121882525
GO:0042301phosphate binding0.00249169833156373
GO:0015198oligopeptide transporter activity0.00249169833156373
GO:0019538protein metabolic process0.00303212289754489
GO:0015197peptide transporter activity0.00314713046787477
GO:0042288MHC class I protein binding0.00344958683718131
GO:0002483antigen processing and presentation of endogenous peptide antigen0.00583164475744578
GO:0019885antigen processing and presentation of endogenous peptide antigen via MHC class I0.00583164475744578
GO:0006857oligopeptide transport0.00604832873003494
GO:0042605peptide antigen binding0.00611274679452986
GO:0019883antigen processing and presentation of endogenous antigen0.00611274679452986
GO:0005737cytoplasm0.00663599333603718
GO:0042287MHC protein binding0.00746948551180881
GO:0043231intracellular membrane-bound organelle0.011881802746805
GO:0043227membrane-bound organelle0.011881802746805
GO:0015833peptide transport0.011881802746805
GO:0005788endoplasmic reticulum lumen0.0190872887198677
GO:0006959humoral immune response0.0219186774220755
GO:0043229intracellular organelle0.0241778826458626
GO:0043226organelle0.0241778826458626
GO:0016836hydro-lyase activity0.0248247132780344
GO:0043170macromolecule metabolic process0.0264901850198828
GO:0016835carbon-oxygen lyase activity0.0264901850198828
GO:0002474antigen processing and presentation of peptide antigen via MHC class I0.0264901850198828
GO:0046982protein heterodimerization activity0.0264901850198828
GO:0048002antigen processing and presentation of peptide antigen0.0264901850198828
GO:0044267cellular protein metabolic process0.0329518394413252
GO:0044260cellular macromolecule metabolic process0.0336207880593579
GO:0042803protein homodimerization activity0.03784391734532
GO:0005634nucleus0.0395329301440715
GO:0044238primary metabolic process0.0395329301440715
GO:0003823antigen binding0.0404041470685052
GO:0044424intracellular part0.040719536022715
GO:0042277peptide binding0.0460001800729374



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
leukocyte4.65e-50140
nongranular leukocyte2.40e-46119
hematopoietic cell2.80e-41182
hematopoietic stem cell2.14e-40172
angioblastic mesenchymal cell2.14e-40172
hematopoietic lineage restricted progenitor cell2.89e-40124
hematopoietic oligopotent progenitor cell2.38e-37165
hematopoietic multipotent progenitor cell2.38e-37165
lymphocyte8.26e-2553
common lymphoid progenitor8.26e-2553
lymphoid lineage restricted progenitor cell1.45e-2452
myeloid leukocyte1.21e-2076
macrophage dendritic cell progenitor6.89e-2065
monopoietic cell1.42e-1963
monocyte1.42e-1963
monoblast1.42e-1963
promonocyte1.42e-1963
granulocyte monocyte progenitor cell6.63e-1871
connective tissue cell1.06e-16365
CD14-positive, CD16-negative classical monocyte1.15e-1642
mesenchymal cell1.41e-16358
myeloid lineage restricted progenitor cell7.96e-1670
classical monocyte4.50e-1545
myeloid cell1.32e-14112
common myeloid progenitor1.32e-14112
multi fate stem cell2.43e-13430
lymphocyte of B lineage6.99e-1324
pro-B cell6.99e-1324
motile cell2.13e-12390
somatic stem cell2.21e-12436
T cell7.08e-1225
pro-T cell7.08e-1225
stem cell1.52e-11444
mature alpha-beta T cell8.28e-1018
alpha-beta T cell8.28e-1018
immature T cell8.28e-1018
mature T cell8.28e-1018
immature alpha-beta T cell8.28e-1018
native cell1.79e-09722
somatic cell9.82e-09591
B cell1.53e-0814
CD8-positive, alpha-beta T cell4.64e-0711
Uber Anatomy
Ontology termp-valuen
hemolymphoid system4.11e-29112
hematopoietic system5.65e-27102
blood island5.65e-27102
immune system3.90e-19115
bone marrow3.30e-1780
connective tissue3.66e-16375
bone element8.45e-1486
lateral plate mesoderm7.31e-12216
skeletal element5.68e-11101
skeletal system5.68e-11101
blood8.50e-0915
haemolymphatic fluid8.50e-0915
organism substance8.50e-0915
musculoskeletal system3.69e-07167


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
ELF1#199754.258097958807540.0007142416939776840.00573099940667912
GATA3#2625210.89460654288240.0125158291218830.0452830554167652
GTF2F1#296237.643796526054590.00428415496412050.0203461807238316
IRF1#365957.63716375356393.84754333311872e-050.000724154943535027
MEF2C#4208216.52454179704960.005579850077982050.0252449299209135
NANOG#79923211.69791139240510.01091164951956080.0402231315887834
NFKB1#479055.488063424193840.0002008162847462320.00239036379788143
PAX5#507945.335652424942260.002223389586187790.0127783724957003
PRDM1#639379.09857346647654.30606791165081e-060.000136196676748909
RAD21#588536.21302033727380.007751055068811640.031893169976031
REST#597835.790017229676810.009468788694433940.0356968856245889
RFX5#599349.638328661756080.000221480125815720.00249634824736326
SIN3A#2594255.408884726815140.0002159522671657270.00248035179044555
SMARCB1#6598414.60217262492594.30486693344344e-050.000768408815009228
SMC3#912639.02695970695970.002650964449467550.014637276031612
STAT1#6772416.56526999775942.61308619905866e-050.000563626826814306
STAT2#6773452.21101694915252.71660181075469e-071.3976314113961e-05
STAT3#677436.311678998292540.007411172122460540.0306128541883268
TAF1#687253.343046285745290.002394600090870310.0135322568524649
TBP#690853.706770687096390.001428755106721120.00918715395830854
YY1#752843.928936599883080.007193866269917620.0298403447201496
ZEB1#6935310.13305921052630.001895556924357070.0111614179186406
ZNF143#770238.100525931336740.003624870512090980.0183304048521895



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.