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Coexpression cluster:C1026: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=0.920816,0.600139,3.37926,0.481684,0.301904,1.20684,0.554663,0.561282,1.05889,0.355088,1.14354,0.597407,0.152895,1.34165,0.300614,0.322799,0.774423,0.250594,0.491486,0.560708,0.905237,0.405031,0.472508,2.23515,0.385586,0.619829,0.135503,0.470396,0.304828,0.388322,1.09762,0.810962,0.628961,0.154814,1.36232,0.171488,0.735464,0.481208,0.244807,0.518171,0.268162,0.413601,0.0547276,0.299183,0.0775086,1.72504,0.555735,0.440085,0.0498256,0.304949,0.63387,1.39237,0.639783,0.887323,1.03948,0.546236,0.308962,0.514077,0.122557,2.20421,0.85167,0.558065,0.190442,0.746929,1.4101,0.712797,1.12756,1.49516,0.800646,1.33315,0.400869,0.197328,0.0911419,1.03748,0.149081,0.429044,0.127753,0.730167,0.797419,0.379656,0.167664,0.745864,0.575394,0.567311,3.70189,0.237806,0.0757344,0.118789,0.659621,1.59442,1.22073,0.959334,0.827657,1.20395,0.817658,0.239285,0.162291,0.87,0.664183,0.106284,1.27523,0.822041,0.864454,0.778061,0.701386,1.13403,0.762347,1.33446,1.00159,0.286892,0.352381,2.00355,0.336372,0.459808,1.17281,0.265019,1.199,1.0951,0.710479,0.229841,1.02923,0.657218,0.477387,0.586509,1.28328,0.730921,0.548418,0.83262,1.07171,1.25306,0.960022,1.93411,1.08604,0.583225,1.23359,0.113443,0.423593,0.470947,1.19123,2.04907,1.64679,1.15398,0.550118,0.866494,0.703126,1.2618,0.686615,1.88987,0.410382,1.1925,0.283443,0.423488,0.960402,1.03091,0.557588,1.36372,0.643609,0.288769,0.385642,1.67913,1.15277,0.941964,0.796636,0.36101,0.71907,1.40773,0.213234,0.553354,0.0643507
|tfbs_overrepresentation_jaspar=MA0003.1;0.393486,MA0004.1;0.455723,MA0006.1;0.300178,MA0007.1;0.437331,MA0009.1;2.12026,MA0014.1;0.727045,MA0017.1;0.896777,MA0019.1;0.602411,MA0024.1;0.813542,MA0025.1;1.05265,MA0027.1;2.5321,MA0028.1;2.32702,MA0029.1;0.832916,MA0030.1;0.821423,MA0031.1;0.756713,MA0038.1;1.3714,MA0040.1;0.838784,MA0041.1;0.474018,MA0042.1;0.442535,MA0043.1;0.919032,MA0046.1;0.90778,MA0048.1;0.316923,MA0050.1;0.443405,MA0051.1;0.553205,MA0052.1;0.842664,MA0055.1;0.283474,MA0056.1;0,MA0057.1;0.305162,MA0058.1;0.950944,MA0059.1;0.948176,MA0060.1;3.1469,MA0061.1;0.165998,MA0063.1;0,MA0066.1;1.3723,MA0067.1;1.23721,MA0068.1;0.133123,MA0069.1;0.903908,MA0070.1;0.892666,MA0071.1;0.518907,MA0072.1;0.888148,MA0073.1;0.215282,MA0074.1;0.552456,MA0076.1;2.62795,MA0077.1;0.880402,MA0078.1;0.652193,MA0081.1;0.361233,MA0083.1;0.926258,MA0084.1;1.42483,MA0087.1;0.885691,MA0088.1;0.054222,MA0089.1;0,MA0090.1;0.391903,MA0091.1;2.02209,MA0092.1;0.421159,MA0093.1;0.818737,MA0095.1;0,MA0098.1;0,MA0100.1;0.571227,MA0101.1;0.30624,MA0103.1;0.291333,MA0105.1;0.279181,MA0106.1;0.59853,MA0107.1;0.236528,MA0108.2;0.753643,MA0109.1;0,MA0111.1;0.405141,MA0113.1;0.614917,MA0114.1;0.231781,MA0115.1;1.1606,MA0116.1;0.239768,MA0117.1;0.956472,MA0119.1;0.345493,MA0122.1;0.982472,MA0124.1;1.11898,MA0125.1;1.0347,MA0130.1;0,MA0131.1;0.670358,MA0132.1;0,MA0133.1;0,MA0135.1;0.949204,MA0136.1;0.564434,MA0139.1;0.155155,MA0140.1;0.516266,MA0141.1;0.359385,MA0142.1;0.724856,MA0143.1;0.615094,MA0144.1;0.623945,MA0145.1;0.220937,MA0146.1;0.113833,MA0147.1;0.243042,MA0148.1;0.480298,MA0149.1;0.506665,MA0062.2;5.39963,MA0035.2;0.515566,MA0039.2;0.44475,MA0138.2;0.653421,MA0002.2;0.179788,MA0137.2;0.86081,MA0104.2;0.55506,MA0047.2;0.586412,MA0112.2;0.0572179,MA0065.2;0.226158,MA0150.1;0.386144,MA0151.1;0,MA0152.1;0.52279,MA0153.1;1.01778,MA0154.1;0.274121,MA0155.1;0.43752,MA0156.1;0.865715,MA0157.1;0.697424,MA0158.1;0,MA0159.1;0.682702,MA0160.1;0.495355,MA0161.1;0,MA0162.1;0.194027,MA0163.1;0.0104024,MA0164.1;0.627336,MA0080.2;0.303167,MA0018.2;0.599912,MA0099.2;0.523145,MA0079.2;0.13841,MA0102.2;1.46209,MA0258.1;0.209744,MA0259.1;0.25092,MA0442.1;0
}}
}}

Revision as of 19:38, 22 January 2013


Full id: C1026_Fibroblast_mesothelioma_Chondrocyte_epidermoid_Reticulocytes_clear_myxofibrosarcoma



Phase1 CAGE Peaks

Hg19::chr13:60738003..60738103,-p1@DIAPH3
Hg19::chr15:66797627..66797684,+p1@ZWILCH
Hg19::chr15:69706643..69706710,+p1@KIF23
Hg19::chr15:69706713..69706724,+p4@KIF23
Hg19::chr15:69706740..69706754,+p2@KIF23
Hg19::chr16:46655208..46655316,-p1@SHCBP1
Hg19::chr5:137514834..137514865,+p2@KIF20A
Hg19::chr7:36429461..36429486,+p1@ANLN


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
6.67157721853038e-060.004223108379329733200DNA Replication (Reactome):REACT_383
2.59719623007301e-050.008220126068181063315Cell Cycle, Mitotic (Reactome):REACT_152



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:0007010cytoskeleton organization and biogenesis0.000253758630431385
GO:0006996organelle organization and biogenesis0.00299768850949541
GO:0003777microtubule motor activity0.00364784772441998
GO:0000921septin ring assembly0.00364784772441998
GO:0000022mitotic spindle elongation0.00364784772441998
GO:0032185septin cytoskeleton organization and biogenesis0.00364784772441998
GO:0051231spindle elongation0.00364784772441998
GO:0031106septin ring organization0.00364784772441998
GO:0005826contractile ring0.00364784772441998
GO:0044430cytoskeletal part0.00364784772441998
GO:0007018microtubule-based movement0.00364784772441998
GO:0005875microtubule associated complex0.00364784772441998
GO:0030705cytoskeleton-dependent intracellular transport0.00398926605803164
GO:0032153cell division site0.00404014110159463
GO:0032155cell division site part0.00404014110159463
GO:0043232intracellular non-membrane-bound organelle0.00404014110159463
GO:0043228non-membrane-bound organelle0.00404014110159463
GO:0007067mitosis0.00404014110159463
GO:0000087M phase of mitotic cell cycle0.00404014110159463
GO:0051301cell division0.00404014110159463
GO:0016043cellular component organization and biogenesis0.00541511559004266
GO:0005874microtubule0.00541511559004266
GO:0000279M phase0.0054585510817247
GO:0007017microtubule-based process0.00547302045029384
GO:0005856cytoskeleton0.00547302045029384
GO:0000278mitotic cell cycle0.00547302045029384
GO:0022403cell cycle phase0.00673190003874274
GO:0007052mitotic spindle organization and biogenesis0.00734938574349256
GO:0007096regulation of exit from mitosis0.00810540212515731
GO:0010458exit from mitosis0.00810540212515731
GO:0003779actin binding0.00821972114767682
GO:0044446intracellular organelle part0.00857158797561516
GO:0044422organelle part0.00857158797561516
GO:0042169SH2 domain binding0.00986760624313977
GO:0015630microtubule cytoskeleton0.00986760624313977
GO:0007051spindle organization and biogenesis0.00986760624313977
GO:0008092cytoskeletal protein binding0.0128918198713952
GO:0022402cell cycle process0.013414253511694
GO:0005871kinesin complex0.013414253511694
GO:0000776kinetochore0.0144770113713652
GO:0017048Rho GTPase binding0.0145784508666697
GO:0000910cytokinesis0.0151185788309958
GO:0044448cell cortex part0.0195287248205947
GO:0007049cell cycle0.020608139162833
GO:0046907intracellular transport0.0231279426470676
GO:0043234protein complex0.0231279426470676
GO:0005938cell cortex0.025374928519782
GO:0007088regulation of mitosis0.0260052133793836
GO:0043623cellular protein complex assembly0.0262310674601063
GO:0000775chromosome, pericentric region0.0279232946214486
GO:0017016Ras GTPase binding0.0279232946214486
GO:0005819spindle0.0279232946214486
GO:0051649establishment of cellular localization0.0287133850572141
GO:0031267small GTPase binding0.0290343433953052
GO:0051641cellular localization0.0290343433953052
GO:0051020GTPase binding0.0321997196792408
GO:0000226microtubule cytoskeleton organization and biogenesis0.0332532401154693
GO:0019904protein domain specific binding0.0406149369245473
GO:0032991macromolecular complex0.0410585754456491



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>disease_data<br>

Cell Type
Ontology termp-valuen
animal cell4.91e-25679
eukaryotic cell4.91e-25679
epithelial cell1.04e-18253
native cell2.18e-14722
embryonic cell6.08e-11250
squamous epithelial cell2.08e-0763
fibroblast2.23e-0776
Uber Anatomy
Ontology termp-valuen
larynx4.53e-079
Disease
Ontology termp-valuen
cancer7.10e-48235
disease of cellular proliferation3.08e-47239
cell type cancer2.52e-26143
carcinoma2.87e-20106
organ system cancer2.64e-19137
hematologic cancer2.78e-1051
immune system cancer2.78e-1051
leukemia2.09e-0739


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)
MA0003.10.393486
MA0004.10.455723
MA0006.10.300178
MA0007.10.437331
MA0009.12.12026
MA0014.10.727045
MA0017.10.896777
MA0019.10.602411
MA0024.10.813542
MA0025.11.05265
MA0027.12.5321
MA0028.12.32702
MA0029.10.832916
MA0030.10.821423
MA0031.10.756713
MA0038.11.3714
MA0040.10.838784
MA0041.10.474018
MA0042.10.442535
MA0043.10.919032
MA0046.10.90778
MA0048.10.316923
MA0050.10.443405
MA0051.10.553205
MA0052.10.842664
MA0055.10.283474
MA0056.10
MA0057.10.305162
MA0058.10.950944
MA0059.10.948176
MA0060.13.1469
MA0061.10.165998
MA0063.10
MA0066.11.3723
MA0067.11.23721
MA0068.10.133123
MA0069.10.903908
MA0070.10.892666
MA0071.10.518907
MA0072.10.888148
MA0073.10.215282
MA0074.10.552456
MA0076.12.62795
MA0077.10.880402
MA0078.10.652193
MA0081.10.361233
MA0083.10.926258
MA0084.11.42483
MA0087.10.885691
MA0088.10.054222
MA0089.10
MA0090.10.391903
MA0091.12.02209
MA0092.10.421159
MA0093.10.818737
MA0095.10
MA0098.10
MA0100.10.571227
MA0101.10.30624
MA0103.10.291333
MA0105.10.279181
MA0106.10.59853
MA0107.10.236528
MA0108.20.753643
MA0109.10
MA0111.10.405141
MA0113.10.614917
MA0114.10.231781
MA0115.11.1606
MA0116.10.239768
MA0117.10.956472
MA0119.10.345493
MA0122.10.982472
MA0124.11.11898
MA0125.11.0347
MA0130.10
MA0131.10.670358
MA0132.10
MA0133.10
MA0135.10.949204
MA0136.10.564434
MA0139.10.155155
MA0140.10.516266
MA0141.10.359385
MA0142.10.724856
MA0143.10.615094
MA0144.10.623945
MA0145.10.220937
MA0146.10.113833
MA0147.10.243042
MA0148.10.480298
MA0149.10.506665
MA0062.25.39963
MA0035.20.515566
MA0039.20.44475
MA0138.20.653421
MA0002.20.179788
MA0137.20.86081
MA0104.20.55506
MA0047.20.586412
MA0112.20.0572179
MA0065.20.226158
MA0150.10.386144
MA0151.10
MA0152.10.52279
MA0153.11.01778
MA0154.10.274121
MA0155.10.43752
MA0156.10.865715
MA0157.10.697424
MA0158.10
MA0159.10.682702
MA0160.10.495355
MA0161.10
MA0162.10.194027
MA0163.10.0104024
MA0164.10.627336
MA0080.20.303167
MA0018.20.599912
MA0099.20.523145
MA0079.20.13841
MA0102.21.46209
MA0258.10.209744
MA0259.10.25092
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
BRCA1#672512.61514415201491.47177326411908e-050.000349421522917327
CEBPB#105154.981967266140510.001250523778793020.0084059633734546
CHD2#110667.758017125587641.92157406469162e-050.000434294035365349
E2F1#186984.907389214879322.97124777369457e-060.000101476176009446
E2F4#1874812.66806031528441.5050509647149e-091.33434650003277e-07
E2F6#187674.390011265235218.25033297218753e-050.00123997197479104
ELF1#199773.72583571395660.0002503412725512720.00269846136484491
ELK4#2005510.14730103654254.23608403932528e-050.000758334557735847
ETS1#211378.512665806927048.8174082362229e-073.82267039760433e-05
FOS#235366.74846648167084.31702653902356e-050.000770052834686731
GABPB1#255365.300762877136630.000173452943092670.00211133472303676
HEY1#2346284.040111043105711.4081650274634e-050.00033902108645286
IRF1#365976.682518284368414.6709523292352e-060.000145057862121022
IRF3#3661529.3637201321812.31300241196823e-071.22003868133106e-05
MAX#414964.839416631755340.0002917504313705360.00309718675563198
MXI1#460178.716375175164397.48926294096089e-073.31428445886023e-05
NFYA#4800613.81918552487296.49659712753933e-072.94614896831559e-05
NFYB#4801612.56984494015231.13616741401493e-064.66065155350768e-05
PAX5#507954.168478456986140.002847508706107280.0154360511656358
POLR2A#543082.147453176558070.002210725788971910.0127167873250957
POU2F2#545244.553062028871260.007062473846831130.0294591303654124
RFX5#599357.529944266996940.000177917256858560.00215863155077267
SIN3A#2594285.408884726815141.36410592556506e-065.35183541548044e-05
SMARCB1#659836.844768417934030.007473690134633950.0308223315420563
SP1#666785.69838137814098.98832477855329e-073.86309321624414e-05
SREBF1#6720317.62719354018310.0004972605150068210.00439554726422322
TAF1#687283.343046285745296.40776711117462e-050.00104337510028682
TAF7#6879811.43306940492393.41987905000906e-092.81678823425785e-07
TBP#690883.706770687096392.80450451364125e-050.000592075291894437
TFAP2C#702268.106921457395171.48721435420767e-050.000352606537886709



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.

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=Coexpression_cluster:C1026&oldid=2569537"