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{{Coexpression_clusters
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Latest revision as of 03:00, 17 September 2013


Full id: C2194_Mast_CD4_cord_embryonic_hepatoblastoma_cerebellum_lung



Phase1 CAGE Peaks

  Short description
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 clusterSummary:
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.
Analyst: Emmanuel Dimont

link to source dataset
data


No results for this coexpression

Enriched Gene Ontology terms on this co-expression clusterSummary: 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.
Analyst: Erik Arner

link to source dataset
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 clusterSummary: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. Analyst: Hideya Kawaji

links to source dataset

cell_data
uberon_data


Cell Type
Ontology termp-valuen
hematopoietic stem cell7.52e-36168
angioblastic mesenchymal cell7.52e-36168
leukocyte1.02e-33136
hematopoietic oligopotent progenitor cell3.21e-33161
hematopoietic multipotent progenitor cell3.21e-33161
hematopoietic cell3.40e-33177
hematopoietic lineage restricted progenitor cell7.10e-27120
nongranular leukocyte1.16e-24115
myeloid cell1.29e-19108
common myeloid progenitor1.29e-19108
classical monocyte8.49e-1842
CD14-positive, CD16-negative classical monocyte8.49e-1842
myeloid leukocyte3.31e-1672
granulocyte monocyte progenitor cell6.12e-1467
defensive cell8.64e-1448
phagocyte8.64e-1448
myeloid lineage restricted progenitor cell1.41e-1366
nucleate cell1.83e-1355
lymphocyte9.82e-1353
common lymphoid progenitor9.82e-1353
lymphoid lineage restricted progenitor cell1.59e-1252
macrophage dendritic cell progenitor1.10e-1161
monopoietic cell7.01e-1159
monocyte7.01e-1159
monoblast7.01e-1159
promonocyte7.01e-1159
mature alpha-beta T cell1.83e-0718
alpha-beta T cell1.83e-0718
immature T cell1.83e-0718
mature T cell1.83e-0718
immature alpha-beta T cell1.83e-0718
Uber Anatomy
Ontology termp-valuen
hematopoietic system7.20e-1598
blood island7.20e-1598
adult organism8.46e-13114
hemolymphoid system3.54e-11108
bone element1.18e-1082
bone marrow1.21e-1076
skeletal element4.81e-0990
immune system2.08e-0893
neural tube2.45e-0856
neural rod2.45e-0856
future spinal cord2.45e-0856
neural keel2.45e-0856
regional part of forebrain3.82e-0841
forebrain3.82e-0841
anterior neural tube3.82e-0841
future forebrain3.82e-0841
skeletal system6.28e-08100
regional part of nervous system7.19e-0853
regional part of brain7.19e-0853
nervous system3.16e-0789


Overrepresented TFBS (DNA) motifs on this co-expression clusterSummary: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. Analyst: Michiel de Hoon

link to source data
Novel motifs
data

Jaspar motifs
data


Novel motifs



JASPAR motifs

Motifs-log10(p-value)
MA0003.10.0938548
MA0004.10.71247
MA0006.10.532262
MA0007.10.6918
MA0009.11.20602
MA0014.10.0695829
MA0017.11.41335
MA0019.10.873355
MA0024.11.09684
MA0025.11.34373
MA0027.12.83281
MA0028.12.32784
MA0029.11.11704
MA0030.11.10506
MA0031.11.03735
MA0038.11.92746
MA0040.11.12314
MA0041.10.732902
MA0042.10.697662
MA0043.11.20635
MA0046.11.19471
MA0048.10.25531
MA0050.10.69864
MA0051.10.820063
MA0052.11.12718
MA0055.10.125954
MA0056.10
MA0057.10.248209
MA0058.10.605914
MA0059.10.604454
MA0060.11.01899
MA0061.10.360128
MA0063.10
MA0066.10.825101
MA0067.11.53181
MA0068.10.313194
MA0069.11.19071
MA0070.11.17908
MA0071.10.782546
MA0072.11.1744
MA0073.13.86888
MA0074.10.819248
MA0076.12.5647
MA0077.11.16637
MA0078.10.926725
MA0081.10.604638
MA0083.11.21381
MA0084.11.72172
MA0087.11.17185
MA0088.11.02755
MA0089.10
MA0090.11.54523
MA0091.10.715356
MA0092.10.673508
MA0093.10.535768
MA0095.10
MA0098.10
MA0100.10.83965
MA0101.10.539569
MA0103.10.521546
MA0105.10.232357
MA0106.10.869173
MA0107.10.453492
MA0108.21.03412
MA0109.10
MA0111.10.655276
MA0113.10.886811
MA0114.10.447443
MA0115.11.45393
MA0116.10.457606
MA0117.11.24497
MA0119.10.586221
MA0122.11.27173
MA0124.11.41151
MA0125.11.32534
MA0130.10
MA0131.10.94608
MA0132.10
MA0133.10
MA0135.11.23748
MA0136.10.832277
MA0139.10.912459
MA0140.10.779643
MA0141.10.602484
MA0142.11.00381
MA0143.10.887001
MA0144.11.09982
MA0145.10.195821
MA0146.10.221129
MA0147.10.46175
MA0148.10.739888
MA0149.10.769072
MA0062.22.51225
MA0035.20.778873
MA0039.21.13403
MA0138.20.928035
MA0002.20.379056
MA0137.20.558189
MA0104.20.392359
MA0047.20.856092
MA0112.20.551048
MA0065.20.199162
MA0150.10.633493
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.10.229241
MA0155.10.180766
MA0156.11.37856
MA0157.10.97481
MA0158.10
MA0159.10.462502
MA0160.10.756582
MA0161.10
MA0162.10.309472
MA0163.10.0725493
MA0164.10.90014
MA0080.21.32578
MA0018.20.870662
MA0099.20.7872
MA0079.20.0626799
MA0102.21.75932
MA0258.11.07498
MA0259.10.471671
MA0442.10



ENCODE TF ChIP-seq peak enrichment analysisSummary: 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.
Analyst: Erik Arner

link to source dataset

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 clusterSummary:Co-expression clusters are compared against FANTOM5 samples to obtain relative expression.
Analyst:NA

link to data source
data


This analysis result is provided for C0 - C305 clusters.