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Coexpression cluster:C2194: Difference between revisions

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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C2194_Mast_CD4_cord_embryonic_hepatoblastoma_cerebellum_lung
|full_id=C2194_Mast_CD4_cord_embryonic_hepatoblastoma_cerebellum_lung
|gostat_on_coexpression_clusters=GO:0004221!ubiquitin thiolesterase activity!0.0344053391563105!10600$GO:0004843!ubiquitin-specific protease activity!0.0344053391563105!10600$GO:0019783!small conjugating protein-specific protease activity!0.0344053391563105!10600$GO:0004197!cysteine-type endopeptidase activity!0.0344053391563105!10600$GO:0016790!thiolester hydrolase activity!0.0344053391563105!10600$GO:0006511!ubiquitin-dependent protein catabolic process!0.0344053391563105!10600$GO:0043632!modification-dependent macromolecule catabolic process!0.0344053391563105!10600$GO:0019941!modification-dependent protein catabolic process!0.0344053391563105!10600$GO:0051603!proteolysis involved in cellular protein catabolic process!0.0344053391563105!10600$GO:0044257!cellular protein catabolic process!0.0344053391563105!10600$GO:0008234!cysteine-type peptidase activity!0.0344053391563105!10600$GO:0030163!protein catabolic process!0.0375505318105106!10600$GO:0043285!biopolymer catabolic process!0.0442038239636262!10600$GO:0044265!cellular macromolecule catabolic process!0.0463263864358884!10600$GO:0006512!ubiquitin cycle!0.0463263864358884!10600$GO:0009057!macromolecule catabolic process!0.0494432915342046!10600
|gostat_on_coexpression_clusters=GO:0004221!ubiquitin thiolesterase activity!0.0344053391563105!10600$GO:0004843!ubiquitin-specific protease activity!0.0344053391563105!10600$GO:0019783!small conjugating protein-specific protease activity!0.0344053391563105!10600$GO:0004197!cysteine-type endopeptidase activity!0.0344053391563105!10600$GO:0016790!thiolester hydrolase activity!0.0344053391563105!10600$GO:0006511!ubiquitin-dependent protein catabolic process!0.0344053391563105!10600$GO:0043632!modification-dependent macromolecule catabolic process!0.0344053391563105!10600$GO:0019941!modification-dependent protein catabolic process!0.0344053391563105!10600$GO:0051603!proteolysis involved in cellular protein catabolic process!0.0344053391563105!10600$GO:0044257!cellular protein catabolic process!0.0344053391563105!10600$GO:0008234!cysteine-type peptidase activity!0.0344053391563105!10600$GO:0030163!protein catabolic process!0.0375505318105106!10600$GO:0043285!biopolymer catabolic process!0.0442038239636262!10600$GO:0044265!cellular macromolecule catabolic process!0.0463263864358884!10600$GO:0006512!ubiquitin cycle!0.0463263864358884!10600$GO:0009057!macromolecule catabolic process!0.0494432915342046!10600

Revision as of 14:53, 12 September 2012


Full id: C2194_Mast_CD4_cord_embryonic_hepatoblastoma_cerebellum_lung



Phase1 CAGE Peaks

Hg19::chr12:123011476..123011527,-p1@RSRC2
Hg19::chr12:123011536..123011547,-p2@RSRC2
Hg19::chr21:30396966..30397025,+p1@USP16
Hg19::chr3:14693247..14693293,+p1@C3orf19


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 activity0.0344053391563105
GO:0004843ubiquitin-specific protease activity0.0344053391563105
GO:0019783small conjugating protein-specific protease activity0.0344053391563105
GO:0004197cysteine-type endopeptidase activity0.0344053391563105
GO:0016790thiolester hydrolase activity0.0344053391563105
GO:0006511ubiquitin-dependent protein catabolic process0.0344053391563105
GO:0043632modification-dependent macromolecule catabolic process0.0344053391563105
GO:0019941modification-dependent protein catabolic process0.0344053391563105
GO:0051603proteolysis involved in cellular protein catabolic process0.0344053391563105
GO:0044257cellular protein catabolic process0.0344053391563105
GO:0008234cysteine-type peptidase activity0.0344053391563105
GO:0030163protein catabolic process0.0375505318105106
GO:0043285biopolymer catabolic process0.0442038239636262
GO:0044265cellular macromolecule catabolic process0.0463263864358884
GO:0006512ubiquitin cycle0.0463263864358884
GO:0009057macromolecule catabolic process0.0494432915342046



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
hematopoietic stem cell1.99e-35172
angioblastic mesenchymal cell1.99e-35172
leukocyte3.30e-33140
hematopoietic oligopotent progenitor cell1.29e-32165
hematopoietic multipotent progenitor cell1.29e-32165
hematopoietic cell7.31e-32182
hematopoietic lineage restricted progenitor cell3.15e-26124
nongranular leukocyte7.47e-24119
myeloid cell8.10e-19112
common myeloid progenitor8.10e-19112
CD14-positive, CD16-negative classical monocyte3.70e-1742
classical monocyte4.48e-1645
myeloid leukocyte1.77e-1576
lymphocyte5.22e-1353
common lymphoid progenitor5.22e-1353
granulocyte monocyte progenitor cell8.10e-1371
myeloid lineage restricted progenitor cell8.71e-1370
lymphoid lineage restricted progenitor cell8.81e-1352
macrophage dendritic cell progenitor9.60e-1165
monopoietic cell5.37e-1063
monocyte5.37e-1063
monoblast5.37e-1063
promonocyte5.37e-1063
mature alpha-beta T cell3.54e-0718
alpha-beta T cell3.54e-0718
immature T cell3.54e-0718
mature T cell3.54e-0718
immature alpha-beta T cell3.54e-0718
Uber Anatomy
Ontology termp-valuen
hematopoietic system3.56e-14102
blood island3.56e-14102
adult organism7.12e-13115
hemolymphoid system1.37e-10112
bone marrow4.56e-1080
bone element4.83e-1086
skeletal element6.30e-08101
skeletal system6.30e-08101
neural tube8.28e-0857
neural rod8.28e-0857
future spinal cord8.28e-0857
neural keel8.28e-0857
anterior neural tube2.72e-0742
regional part of forebrain2.72e-0741
forebrain2.72e-0741
future forebrain2.72e-0741


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#467211.23158726300440.01119559039922220.0411217649892511
BCLAF1#9774210.82632380506090.01202203816432580.0436461794362993
BRCA1#672315.13817298241780.0004682184421431190.00430005855425477
CEBPB#105135.978360719368610.007153832484726970.0297179551677499
CHD2#1106410.34402283411698.73193255208051e-050.00128916356206776
ELF1#199744.258097958807540.003041525565781240.0160609712086473
ELK4#2005416.2356816584681.43847748454449e-050.000342919767195485
EP300#203335.08045629466740.01144298405398240.0418743451861901
ESRRA#21011120.9600785340310.008241662461779040.032479943618948
ETS1#211337.296570691651750.00400857377511390.0191997907130989
FOS#235336.74846648167080.005032452776317940.0234552095459599
FOXA1#316938.311064812039090.002740138182109850.0150342680116296
GABPB1#255347.067683836182170.0004006876864423170.00389822275587789
GTF2B#2959323.95787245074320.0001197754562855920.00162394247423224
GTF2F1#2962412.73966087675773.79492332235515e-050.000716705238451085
HEY1#2346244.040111043105710.00375304636917980.0185641948352169
IRF1#365935.727872815172930.008097114790333330.0319960110324488
IRF4#3662210.95725634337210.01174530180688030.0428230956679621
JUND#372735.245997956403270.01043432751748420.0386724415912039
MAX#414934.839416631755340.01315737137836840.0465984844988102
MXI1#460137.471178721569470.003741314738550960.0186270281727379
MYC#460945.22228187160940.001344309395272740.00886073391813754
NFKB1#479045.488063424193840.001102199566301980.00766804026811966
NFYA#4800313.81918552487290.0006132411806734510.00508465351447718
NFYB#4801312.56984494015230.000811456397697350.00618460882428034
NR2C2#7182216.30730545262040.005411825344648220.0245528074356957
NR3C1#2908311.22976749837980.001131672068063850.00775275166392396
NRF1#4899412.21027944771094.49717228915276e-050.000792307990396129
POU2F2#545249.106124057742520.000145395665174930.00188142459115407
PPARGC1A#10891187.51278409090910.01137812176383720.0417042064607776
REST#597837.237521537096020.004104697304192610.0195722267156358
RFX5#599339.035933120396320.002144561191324070.0123825644770397
RXRA#6256315.055962854350.0004758307997303580.00433679142098254
SIN3A#2594245.408884726815140.001168172384885160.00794754450557103
SMARCB1#6598313.68953683586810.0006305783409379340.00517987819326859
SP2#6668213.07676524692230.008330036536614940.0328034646449051
SPI1#668836.153242631392040.006580387113059030.0280911117801256
STAT1#6772210.35329374859960.01310777476171260.0464874656458334
STAT2#6773232.63188559322030.001379588775125520.0089827226985869
TAF1#687243.343046285745290.008005664898701650.032139290269287
TBP#690843.706770687096390.005296377814784350.0243591863043096
USF2#739239.74414803880220.001718341848410070.0107154229941545
XRCC4#751811074.575581395350.0009302828080034460.00674332358308384
YY1#752844.911170749853860.00171871838055440.0106655513337327
ZNF143#7702413.50087655222793.00867915035614e-050.000619892368877579
ZNF263#1012736.166381227758010.006539814347975980.027961340757697



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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