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Coexpression cluster:C1868: Difference between revisions

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|tfbs_overrepresentation_jaspar=MA0003.1;1.04569,MA0004.1;0.626788,MA0006.1;0.452993,MA0007.1;0.606704,MA0009.1;1.11255,MA0014.1;1.45664,MA0017.1;0.496101,MA0019.1;0.784036,MA0024.1;2.29497,MA0025.1;1.24931,MA0027.1;2.73598,MA0028.1;2.0635,MA0029.1;1.02437,MA0030.1;1.01252,MA0031.1;0.945567,MA0038.1;0.736268,MA0040.1;1.03042,MA0041.1;0.64667,MA0042.1;0.612397,MA0043.1;1.11288,MA0046.1;1.10134,MA0048.1;0.195817,MA0050.1;0.613347,MA0051.1;0.731787,MA0052.1;1.03442,MA0055.1;0.603517,MA0056.1;0,MA0057.1;0.189508,MA0058.1;0.523638,MA0059.1;0.522232,MA0060.1;3.25531,MA0061.1;0.291022,MA0063.1;0,MA0066.1;0.736721,MA0067.1;1.43651,MA0068.1;0.247962,MA0069.1;1.09737,MA0070.1;1.08584,MA0071.1;0.695094,MA0072.1;1.0812,MA0073.1;0.111822,MA0074.1;0.730989,MA0076.1;2.29573,MA0077.1;1.07324,MA0078.1;0.836493,MA0081.1;0.522409,MA0083.1;1.12028,MA0084.1;1.62584,MA0087.1;1.07867,MA0088.1;0.412364,MA0089.1;0,MA0090.1;0.556637,MA0091.1;0.629594,MA0092.1;0.588959,MA0093.1;0.456342,MA0095.1;0,MA0098.1;0,MA0100.1;0.750974,MA0101.1;0.459973,MA0103.1;0.442769,MA0105.1;0.175503,MA0106.1;0.779931,MA0107.1;0.985964,MA0108.2;0.94238,MA0109.1;0,MA0111.1;0.5713,MA0113.1;0.797251,MA0114.1;0.372523,MA0115.1;1.35895,MA0116.1;0.994489,MA0117.1;1.1512,MA0119.1;0.504689,MA0122.1;1.17777,MA0124.1;1.31673,MA0125.1;1.23103,MA0130.1;0,MA0131.1;0.855546,MA0132.1;0,MA0133.1;0,MA0135.1;1.14377,MA0136.1;0.743749,MA0139.1;0.759606,MA0140.1;0.692258,MA0141.1;0.520334,MA0142.1;0.912455,MA0143.1;0.797437,MA0144.1;0.356507,MA0145.1;0.442008,MA0146.1;0.333008,MA0147.1;0.386018,MA0148.1;0.653474,MA0149.1;0.681935,MA0062.2;2.17426,MA0035.2;0.691506,MA0039.2;0.527987,MA0138.2;0.837782,MA0002.2;0.30855,MA0137.2;0.47779,MA0104.2;0.320919,MA0047.2;0.767096,MA0112.2;0.425004,MA0065.2;0.146576,MA0150.1;0.550239,MA0151.1;0,MA0152.1;0.69926,MA0153.1;1.21379,MA0154.1;0.172764,MA0155.1;0.813062,MA0156.1;1.20729,MA0157.1;0.883854,MA0158.1;0,MA0159.1;0.386729,MA0160.1;0.669748,MA0161.1;0,MA0162.1;0.469165,MA0163.1;0.168633,MA0164.1;0.810347,MA0080.2;0.456437,MA0018.2;0.781393,MA0099.2;0.699641,MA0079.2;0.340387,MA0102.2;1.66336,MA0258.1;0.345771,MA0259.1;0.395396,MA0442.1;0
}}
}}

Revision as of 20:14, 22 January 2013


Full id: C1868_hereditary_teratocarcinoma_adrenal_epitheloid_large_acantholytic_Reticulocytes



Phase1 CAGE Peaks

Hg19::chr20:35402135..35402207,-p1@DSN1
Hg19::chr3:155588375..155588512,+p1@GMPS
Hg19::chr3:179280702..179280769,+p1@ACTL6A
Hg19::chr3:186524234..186524303,-p1@RFC4
Hg19::chr7:7680052..7680078,-p2@RPA3


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
1.54262472139839e-050.00195296289729036236DNA replication (KEGG):03030
2.75970978623047e-050.0024955661352627248Nucleotide excision repair (KEGG):03420
6.20063328622183e-060.00195296289729036223Mismatch repair (KEGG):03430
2.10736705709464e-050.00222327224523484242DNA Replication (Wikipathways):WP1806
0.0001652210940222060.01045849525160562117Cell Cycle Checkpoints (Reactome):REACT_1538
0.000138170770235490.00971801083989612107DNA Repair (Reactome):REACT_216
3.3531346989962e-060.001952962897290363200DNA Replication (Reactome):REACT_383
1.30932089172023e-050.001952962897290363315Cell Cycle, Mitotic (Reactome):REACT_152
7.14406195160067e-050.00565273901920403277Chromosome Maintenance (Reactome):REACT_22172
1.37386321379175e-050.00195296289729036234{PCNA,34} (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:0005657replication fork0.00144153184862913
GO:0044427chromosomal part0.00208358897940201
GO:0005694chromosome0.00212435165266929
GO:0003922GMP synthase (glutamine-hydrolyzing) activity0.00494524902861179
GO:0003921GMP synthase activity0.00494524902861179
GO:0043234protein complex0.00675618320106279
GO:0022616DNA strand elongation0.0077899374882706
GO:0006271DNA strand elongation during DNA replication0.0077899374882706
GO:0006259DNA metabolic process0.0077899374882706
GO:0000444MIS12/MIND type complex0.0077899374882706
GO:0006177GMP biosynthetic process0.0077899374882706
GO:0046037GMP metabolic process0.0077899374882706
GO:0032991macromolecular complex0.0077899374882706
GO:0003689DNA clamp loader activity0.0077899374882706
GO:0033170DNA-protein loading ATPase activity0.0077899374882706
GO:0035267NuA4 histone acetyltransferase complex0.0077899374882706
GO:0005662DNA replication factor A complex0.0077899374882706
GO:0044446intracellular organelle part0.0077899374882706
GO:0044422organelle part0.0077899374882706
GO:0005663DNA replication factor C complex0.0077899374882706
GO:0009113purine base biosynthetic process0.0077899374882706
GO:0043189H4/H2A histone acetyltransferase complex0.0077899374882706
GO:0006260DNA replication0.0077899374882706
GO:0000777condensed chromosome kinetochore0.0079091381939718
GO:0000779condensed chromosome, pericentric region0.0079091381939718
GO:0006281DNA repair0.00838626150757864
GO:0006144purine base metabolic process0.00915301729194821
GO:0006974response to DNA damage stimulus0.0101406475116562
GO:0000123histone acetyltransferase complex0.0110763505871249
GO:0046112nucleobase biosynthetic process0.0115300861109198
GO:0043601nuclear replisome0.0115808778598948
GO:0030894replisome0.0115808778598948
GO:0009719response to endogenous stimulus0.0119433952415913
GO:0016884carbon-nitrogen ligase activity, with glutamine as amido-N-donor0.0119985824167592
GO:0043596nuclear replication fork0.0119985824167592
GO:0009112nucleobase metabolic process0.0150556898479508
GO:0006541glutamine metabolic process0.0150556898479508
GO:0009167purine ribonucleoside monophosphate metabolic process0.0150556898479508
GO:0009168purine ribonucleoside monophosphate biosynthetic process0.0150556898479508
GO:0009127purine nucleoside monophosphate biosynthetic process0.0150556898479508
GO:0009126purine nucleoside monophosphate metabolic process0.0150556898479508
GO:0006139nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0151320209506773
GO:0005634nucleus0.0169232163420361
GO:0000776kinetochore0.0173900211118302
GO:0009161ribonucleoside monophosphate metabolic process0.0174616809728728
GO:0009156ribonucleoside monophosphate biosynthetic process0.0174616809728728
GO:0005524ATP binding0.0174616809728728
GO:0032559adenyl ribonucleotide binding0.0175052163371643
GO:0046148pigment biosynthetic process0.0175379048208526
GO:0043232intracellular non-membrane-bound organelle0.0175379048208526
GO:0043228non-membrane-bound organelle0.0175379048208526
GO:0009124nucleoside monophosphate biosynthetic process0.0175379048208526
GO:0009123nucleoside monophosphate metabolic process0.0175379048208526
GO:0030554adenyl nucleotide binding0.0175379048208526
GO:0042440pigment metabolic process0.01883633608628
GO:0000793condensed chromosome0.0228912471177436
GO:0019748secondary metabolic process0.0229207899784339
GO:0044424intracellular part0.0233753563053392
GO:0007059chromosome segregation0.0246419545531916
GO:0003697single-stranded DNA binding0.0250261873742735
GO:0006338chromatin remodeling0.0250261873742735
GO:0032553ribonucleotide binding0.0250261873742735
GO:0032555purine ribonucleotide binding0.0250261873742735
GO:0044454nuclear chromosome part0.025724233707556
GO:0044428nuclear part0.025724233707556
GO:0017076purine nucleotide binding0.0264993261056813
GO:0000775chromosome, pericentric region0.0279241051497402
GO:0006950response to stress0.0291770609694501
GO:0009064glutamine family amino acid metabolic process0.0291770609694501
GO:0008094DNA-dependent ATPase activity0.0291770609694501
GO:0000228nuclear chromosome0.0342790856501484
GO:0000166nucleotide binding0.0374130305697161
GO:0005622intracellular0.0374130305697161
GO:0003682chromatin binding0.0391576713235763
GO:0043231intracellular membrane-bound organelle0.0398889373448718
GO:0043227membrane-bound organelle0.0398889373448718
GO:0048015phosphoinositide-mediated signaling0.0408986044603046
GO:0046483heterocycle metabolic process0.0408986044603046
GO:0009152purine ribonucleotide biosynthetic process0.0456158013559859
GO:0009150purine ribonucleotide metabolic process0.0469285643966661
GO:0009260ribonucleotide biosynthetic process0.0469285643966661
GO:0043566structure-specific DNA binding0.0469285643966661
GO:0006164purine nucleotide biosynthetic process0.0469285643966661
GO:0001558regulation of cell growth0.0472364507656931
GO:0006261DNA-dependent DNA replication0.0475367888405612
GO:0006163purine nucleotide metabolic process0.047558702635796
GO:0009259ribonucleotide metabolic process0.047558702635796



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><br>disease_data<br>

Cell Type
Ontology termp-valuen
epithelial cell6.63e-15253
animal cell5.42e-11679
eukaryotic cell5.42e-11679
native cell8.03e-08722
Disease
Ontology termp-valuen
cancer1.49e-64235
disease of cellular proliferation6.17e-63239
cell type cancer2.64e-36143
carcinoma7.18e-33106
organ system cancer1.65e-29137
hematologic cancer1.93e-1851
immune system cancer1.93e-1851
leukemia6.88e-1539
myeloid leukemia1.30e-1131
disease of anatomical entity2.99e-0939
adenocarcinoma9.03e-0725


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)
MA0003.11.04569
MA0004.10.626788
MA0006.10.452993
MA0007.10.606704
MA0009.11.11255
MA0014.11.45664
MA0017.10.496101
MA0019.10.784036
MA0024.12.29497
MA0025.11.24931
MA0027.12.73598
MA0028.12.0635
MA0029.11.02437
MA0030.11.01252
MA0031.10.945567
MA0038.10.736268
MA0040.11.03042
MA0041.10.64667
MA0042.10.612397
MA0043.11.11288
MA0046.11.10134
MA0048.10.195817
MA0050.10.613347
MA0051.10.731787
MA0052.11.03442
MA0055.10.603517
MA0056.10
MA0057.10.189508
MA0058.10.523638
MA0059.10.522232
MA0060.13.25531
MA0061.10.291022
MA0063.10
MA0066.10.736721
MA0067.11.43651
MA0068.10.247962
MA0069.11.09737
MA0070.11.08584
MA0071.10.695094
MA0072.11.0812
MA0073.10.111822
MA0074.10.730989
MA0076.12.29573
MA0077.11.07324
MA0078.10.836493
MA0081.10.522409
MA0083.11.12028
MA0084.11.62584
MA0087.11.07867
MA0088.10.412364
MA0089.10
MA0090.10.556637
MA0091.10.629594
MA0092.10.588959
MA0093.10.456342
MA0095.10
MA0098.10
MA0100.10.750974
MA0101.10.459973
MA0103.10.442769
MA0105.10.175503
MA0106.10.779931
MA0107.10.985964
MA0108.20.94238
MA0109.10
MA0111.10.5713
MA0113.10.797251
MA0114.10.372523
MA0115.11.35895
MA0116.10.994489
MA0117.11.1512
MA0119.10.504689
MA0122.11.17777
MA0124.11.31673
MA0125.11.23103
MA0130.10
MA0131.10.855546
MA0132.10
MA0133.10
MA0135.11.14377
MA0136.10.743749
MA0139.10.759606
MA0140.10.692258
MA0141.10.520334
MA0142.10.912455
MA0143.10.797437
MA0144.10.356507
MA0145.10.442008
MA0146.10.333008
MA0147.10.386018
MA0148.10.653474
MA0149.10.681935
MA0062.22.17426
MA0035.20.691506
MA0039.20.527987
MA0138.20.837782
MA0002.20.30855
MA0137.20.47779
MA0104.20.320919
MA0047.20.767096
MA0112.20.425004
MA0065.20.146576
MA0150.10.550239
MA0151.10
MA0152.10.69926
MA0153.11.21379
MA0154.10.172764
MA0155.10.813062
MA0156.11.20729
MA0157.10.883854
MA0158.10
MA0159.10.386729
MA0160.10.669748
MA0161.10
MA0162.10.469165
MA0163.10.168633
MA0164.10.810347
MA0080.20.456437
MA0018.20.781393
MA0099.20.699641
MA0079.20.340387
MA0102.21.66336
MA0258.10.345771
MA0259.10.395396
MA0442.10



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
E2F1#186954.907389214879320.0003512818099256460.00353070165978486
E2F4#1874512.66806031528443.06319883889696e-060.000103499651742336
E2F6#187655.017155731697390.0003144978599297790.00322967964534967
ELF1#199754.258097958807540.0007142416939776840.00573496488639466
ELK4#200539.741408995080820.00212558656574340.0122872715636063
ETS1#211335.83725655332140.009253279045631430.0349765910331777
GABPB1#255357.067683836182175.6685482528729e-050.00094889807818848
HEY1#2346254.040111043105710.0009288852205177990.00674583433319369
HMGN3#932446.542838178680470.00100801277768350.00722106087444182
IRF1#365946.109731002851120.001315525264767990.00881114237972837
IRF3#3661218.79278088459580.004339629777121510.0205899779344354
MAX#414956.452555509007128.93743970843928e-050.0013073070948315
MXI1#460135.976942977255580.008653004889366880.0329544972337304
MYC#460955.22228187160940.0002573944848850610.00276649404208201
NANOG#79923211.69791139240510.01091164951956080.0402302313754867
NFKB1#479044.390450739355070.004707732692524960.0222073574830449
PAX5#507945.335652424942260.002223389586187790.012780482414655
POU2F2#545235.463674434645510.01115650094469780.0410200247197074
REST#597835.790017229676810.009468788694433940.0357046186394911
RFX5#599337.228746496317060.00502918278958660.0234682463411659
SIN3A#2594255.408884726815140.0002159522671657270.00248280920635418
SP2#6668210.46141219753790.01353191183347140.0477839917492534
TAF1#687253.343046285745290.002394600090870310.0135461834519773
TAF7#687936.859841642954350.005843286407019040.0262503006307064
TBP#690853.706770687096390.001428755106721120.00919507977513232
THAP1#55145318.82148676171080.0003085221948150010.00317518225308276
TRIM28#10155311.15431502715750.001433159271529250.00920244212476135
YY1#752854.911170749853860.00034993140821360.00352765312185522
ZBTB7A#5134145.881527446300720.001524947561042230.00971536621287683
ZNF143#7702410.80070124178230.0001415223430863190.00184432892308361



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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