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Coexpression cluster:C1374: Difference between revisions

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{{Coexpression_clusters
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893393,0.305952,0.356524,0.159817,0.532764,0.730276,0.319704,0.555004,0.607569,0.773067,0.283145,0.597394,0.452272,0.628973,0.594475,0.416321,0.365565,0.47205,0.610358,0.331346,0.578885,0.474879,0.868553,0.518205,0.424119,0.237985,0.519279,0.515179,0.745866,0.623664,0.171067,0.438945,0.619652,0.706112,0.754688,0.39196,0.758981,0.355152,0.346355,0.712437,0.841498,0.520214,0.348678,0.486574,0.809543,0.722202,0.639482,0.471879,0.234123,0.474504,0.621275,0.727464,0.589415,0.202106,0.356483,0.28925,0.624316,0.55481,0.443148,0.509842,0.866311,0.368631,0.321667,0.149733,0.477082,0.368449,0.066291,0.343349,0.450702,0.341084,0.138667,0.459605,0.298707,0.345583,0.299527,0.390707,0.372757,0.172033,0.181635,0.304651,0.115749,0.613566,0.445744,0.371991,0.694395,0.326635,0.349721,0.39301,0.396235,0.566617,0.524829,0.388491,0.357781,0.338712,0.231439,0.359148,0.0641227,0.177916,0.232711,0.327419,0.402268,0.479755,0.163801,0.245045,0.373321,0.433875,0.395243,0.130132,0.373481,0.462042,0.213394,0.270174,0.406219,0.298,0.40549,0.30902,0.0755079,0.12783,0.101672,0.0890286,0.465261,0.0108985,0.578088,0.285875,0.225945,0.18761,0.20516,0.115576,0.385234,0.291842,0.392097,0.352327,0.232997,0.451856,0.521039,0.328594,0.294205,0.120228,0.278746,0.387086,0.232479,0.334662,0.336321,0.139427,0.450171,0.454978,0.366035,0.381922,0.372037,0.263608,0.3488,0.43615,0.218495,0.398705,0.431643,0.316114,0.360691,0.26003,0.35537,0.423126,0.288449,0.244977,0.447896,0.395958,0.314638,0.322324,0.0181701,0.363414,0.524458,0.141901,0.388728,0.157712,0.3633,0.202084,0.104337,0.104656,0.279419,0.149946,0.0797883,0.104584,0.537494,0.454949,0.378002,0.340219,0.412672,0.343186,0.155969,0.186603,0.124175,0.228962,0.12366,0.198264,0.128253,0.14669,0.240899,0.206424,0.0862744,0.129421,0.171188,0.0721407,0.251724,0.36701,0.504058,0.491191,0.573638,0.263371,0.457065,0.446399,0.360168,0.403229,0.507716,0.442751,0.323763,0.486842,0.458912,0.246162,0.295506,0.369944,0.358783,0.491474,0.417013,0.544575,0.21822,0.388558,0.397562,0.21727,0.351946,0.345508,0.484083,0.486223,0.437432,0.302171,0.398223,0.178399,0.547908,0.400541,0.372405,0.182559,0.164471,0.533328,0.313891,0.292462,0.46896,0.137165,0.467981,0.191837,0.395568,0.320916,0.289812,0.384881,0.441686,0.078683,0.592234|tfbs_overrepresentation_for_novel_motifs=1.12961,0.333388,0.436508,0.58616,0.393082,0.584466,0.662701,0.269608,0.267027,0.262261,0.553339,0.707204,0.635275,0.650887,0.391663,0.415981,0.889639,0.336106,0.664996,0.127969,0.436569,0.29639,0.576478,0.387783,0.483957,0.730467,0.585619,2.40434,1.02557,0.547818,0.530785,0.92701,0.302275,0.225641,0.35719,0.134746,0.93226,0.585658,0.329602,1.28576,0.355745,0.513952,0.0979105,0.390088,0.354447,0.468392,0.66382,0.542147,0.630853,0.396429,0.745008,0.675919,0.455399,1.00488,1.15929,0.653901,0.400834,0.62023,0.547548,0.619193,0.968558,0.666252,0.267534,0.861462,0.684675,0.826413,1.24834,1.61834,0.916468,1.45553,1.25018,0.75612,0.882224,1.15727,0.624519,0.594475,1.68655,0.84426,0.913168,0.477584,0.240887,0.86037,0.684313,0.749276,1.10535,1.55864,1.29353,0.181871,0.771626,1.71797,1.34233,1.07807,0.94406,0.30974,0.393853,0.864356,0.234532,0.987239,3.04905,0.166235,0.881389,0.938327,0.981588,0.893363,0.814675,2.321,0.877269,0.647343,1.21459,0.982236,1.13818,0.978783,0.430775,1.38333,1.29401,0.352243,0.800507,0.529546,0.824029,0.312699,1.14892,0.769145,0.581628,0.695878,1.40534,0.845034,0.656181,0.949126,1.1919,0.324369,1.07876,0.53374,1.20639,0.692462,1.35529,0.175219,0.524606,0.57483,1.31259,2.17352,1.7705,1.27501,0.657956,0.983666,0.816466,0.611524,0.799467,2.01411,0.510514,1.49651,0.8388,0.639143,1.07915,0.258882,0.665754,1.48627,0.755083,1.75096,0.484017,0.454152,1.27379,1.06043,0.912368,0.457485,0.83286,0.683502,0.29379,0.661335,0.152397|tfbs_overrepresentation_jaspar=MA0003.1;0.176622,MA0004.1;0.558729,MA0006.1;1.79433,MA0007.1;1.33289,MA0009.1;1.03681,MA0014.1;0.108006,MA0017.1;0.432438,MA0019.1;0.7124,MA0024.1;0.929647,MA0025.1;1.17262,MA0027.1;2.65688,MA0028.1;1.05129,MA0029.1;0.949428,MA0030.1;0.937696,MA0031.1;2.02362,MA0038.1;0.665566,MA0040.1;0.955415,MA0041.1;0.578072,MA0042.1;0.544748,MA0043.1;1.03713,MA0046.1;1.02569,MA0048.1;0.464411,MA0050.1;0.545671,MA0051.1;0.661179,MA0052.1;0.959373,MA0055.1;0.0586456,MA0056.1;0,MA0057.1;0.450439,MA0058.1;0.458909,MA0059.1;0.457555,MA0060.1;0.267412,MA0061.1;0.23892,MA0063.1;0,MA0066.1;0.66601,MA0067.1;1.35893,MA0068.1;0.199491,MA0069.1;1.02175,MA0070.1;1.01032,MA0071.1;0.625297,MA0072.1;1.00572,MA0073.1;0.00563817,MA0074.1;0.660398,MA0076.1;2.07987,MA0077.1;0.997832,MA0078.1;0.763954,MA0081.1;0.457725,MA0083.1;1.04447,MA0084.1;1.5477,MA0087.1;1.00322,MA0088.1;0.0971959,MA0089.1;0,MA0090.1;0.490736,MA0091.1;0.561458,MA0092.1;0.522012,MA0093.1;0.394379,MA0095.1;0,MA0098.1;0,MA0100.1;0.679972,MA0101.1;0.397846,MA0103.1;0.381434,MA0105.1;0.134725,MA0106.1;0.70837,MA0107.1;0.320267,MA0108.2;0.868347,MA0109.1;0,MA0111.1;0.504913,MA0113.1;0.725375,MA0114.1;0.314898,MA0115.1;1.28169,MA0116.1;0.323925,MA0117.1;1.07516,MA0119.1;0.440684,MA0122.1;1.10154,MA0124.1;1.23968,MA0125.1;1.15445,MA0130.1;0,MA0131.1;0.782708,MA0132.1;0,MA0133.1;0,MA0135.1;1.06778,MA0136.1;0.672893,MA0139.1;0.641617,MA0140.1;0.622527,MA0141.1;0.455728,MA0142.1;0.838805,MA0143.1;0.725558,MA0144.1;0.299851,MA0145.1;0.707171,MA0146.1;0.441872,MA0147.1;0.327615,MA0148.1;0.584698,MA0149.1;0.612449,MA0062.2;1.90691,MA0035.2;0.621793,MA0039.2;0.0313803,MA0138.2;0.765223,MA0002.2;0.255126,MA0137.2;0.414885,MA0104.2;0.735746,MA0047.2;0.695777,MA0112.2;0.332548,MA0065.2;0.354331,MA0150.1;0.484557,MA0151.1;0,MA0152.1;0.629368,MA0153.1;1.13732,MA0154.1;0.132326,MA0155.1;0.0961854,MA0156.1;1.07131,MA0157.1;0.810597,MA0158.1;0,MA0159.1;0.328286,MA0160.1;0.600559,MA0161.1;0,MA0162.1;1.39622,MA0163.1;0.113377,MA0164.1;0.738243,MA0080.2;0.394469,MA0018.2;0.709805,MA0099.2;0.629739,MA0079.2;0.248693,MA0102.2;1.58513,MA0258.1;0.289793,MA0259.1;0.336472,MA0442.1;0}}
|full_id=C1374_CD8_CD4_CD19_granulocyte_CD133_CD34_Osteoblast
|id=C1374
}}

Latest revision as of 11:43, 17 September 2013


Full id: C1374_CD8_CD4_CD19_granulocyte_CD133_CD34_Osteoblast



Phase1 CAGE Peaks

Hg19::chr12:9803369..9803403,-p@chr12:9803369..9803403
-
Hg19::chr16:47007658..47007694,+p@chr16:47007658..47007694
+
Hg19::chr17:55927626..55927653,+p@chr17:55927626..55927653
+
Hg19::chr19:33667825..33667860,-p@chr19:33667825..33667860
-
Hg19::chr1:109642799..109642834,+p1@SCARNA2
Hg19::chr1:109642840..109642861,+p2@SCARNA2


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

No GOStat results

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>

Uber Anatomy
Ontology termp-valuen
adult organism6.95e-28114
neural tube2.89e-1856
neural rod2.89e-1856
future spinal cord2.89e-1856
neural keel2.89e-1856
regional part of nervous system2.29e-1753
regional part of brain2.29e-1753
regional part of forebrain3.79e-1541
forebrain3.79e-1541
anterior neural tube3.79e-1541
future forebrain3.79e-1541
central nervous system9.36e-1481
brain1.98e-1268
future brain1.98e-1268
nervous system3.35e-1289
brain grey matter4.62e-1234
gray matter4.62e-1234
telencephalon5.37e-1234
regional part of telencephalon2.94e-1132
cerebral hemisphere3.62e-1132
neurectoderm7.50e-1086
neural plate1.49e-0982
presumptive neural plate1.49e-0982
regional part of cerebral cortex1.95e-0922
neocortex1.14e-0820
cerebral cortex4.32e-0825
pallium4.32e-0825
pre-chordal neural plate3.75e-0761
blood6.75e-0715
haemolymphatic fluid6.75e-0715
organism substance6.75e-0715


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)
MA0003.10.176622
MA0004.10.558729
MA0006.11.79433
MA0007.11.33289
MA0009.11.03681
MA0014.10.108006
MA0017.10.432438
MA0019.10.7124
MA0024.10.929647
MA0025.11.17262
MA0027.12.65688
MA0028.11.05129
MA0029.10.949428
MA0030.10.937696
MA0031.12.02362
MA0038.10.665566
MA0040.10.955415
MA0041.10.578072
MA0042.10.544748
MA0043.11.03713
MA0046.11.02569
MA0048.10.464411
MA0050.10.545671
MA0051.10.661179
MA0052.10.959373
MA0055.10.0586456
MA0056.10
MA0057.10.450439
MA0058.10.458909
MA0059.10.457555
MA0060.10.267412
MA0061.10.23892
MA0063.10
MA0066.10.66601
MA0067.11.35893
MA0068.10.199491
MA0069.11.02175
MA0070.11.01032
MA0071.10.625297
MA0072.11.00572
MA0073.10.00563817
MA0074.10.660398
MA0076.12.07987
MA0077.10.997832
MA0078.10.763954
MA0081.10.457725
MA0083.11.04447
MA0084.11.5477
MA0087.11.00322
MA0088.10.0971959
MA0089.10
MA0090.10.490736
MA0091.10.561458
MA0092.10.522012
MA0093.10.394379
MA0095.10
MA0098.10
MA0100.10.679972
MA0101.10.397846
MA0103.10.381434
MA0105.10.134725
MA0106.10.70837
MA0107.10.320267
MA0108.20.868347
MA0109.10
MA0111.10.504913
MA0113.10.725375
MA0114.10.314898
MA0115.11.28169
MA0116.10.323925
MA0117.11.07516
MA0119.10.440684
MA0122.11.10154
MA0124.11.23968
MA0125.11.15445
MA0130.10
MA0131.10.782708
MA0132.10
MA0133.10
MA0135.11.06778
MA0136.10.672893
MA0139.10.641617
MA0140.10.622527
MA0141.10.455728
MA0142.10.838805
MA0143.10.725558
MA0144.10.299851
MA0145.10.707171
MA0146.10.441872
MA0147.10.327615
MA0148.10.584698
MA0149.10.612449
MA0062.21.90691
MA0035.20.621793
MA0039.20.0313803
MA0138.20.765223
MA0002.20.255126
MA0137.20.414885
MA0104.20.735746
MA0047.20.695777
MA0112.20.332548
MA0065.20.354331
MA0150.10.484557
MA0151.10
MA0152.10.629368
MA0153.11.13732
MA0154.10.132326
MA0155.10.0961854
MA0156.11.07131
MA0157.10.810597
MA0158.10
MA0159.10.328286
MA0160.10.600559
MA0161.10
MA0162.11.39622
MA0163.10.113377
MA0164.10.738243
MA0080.20.394469
MA0018.20.709805
MA0099.20.629739
MA0079.20.248693
MA0102.21.58513
MA0258.10.289793
MA0259.10.336472
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
BCL3#602317.27355140186920.0004539630608098260.00421997757969892
BCLAF1#9774518.04387300843491.21080990322265e-064.89759006516927e-05
BDP1#558141175.0255681818180.00569994366159920.0256992063578725
BHLHE40#8553214.95727118232580.00701655948451940.0296393162920127
BRF1#29721296.1971153846150.003371429938437640.017221401317641
CCNT2#90555.280167980802190.0005100943974832530.0044674003168766
CEBPB#105156.642623021520680.0001668926180572430.00204482615406855
CHD2#110658.620019028430714.6560374997265e-050.000814935311603714
E2F4#187436.334030157642220.008197175368374340.0323583474429318
EGR1#195864.988179094810146.48943962979974e-050.00105502893134598
ELF1#199753.548414965672950.003446837775721690.0175268654977651
ELK4#2005410.8237877723120.0001950599973010460.00234942579380971
EP300#203355.644951438519330.0003688138931814860.00366948215585226
ETS1#211358.107300768501956.29183579217211e-050.00102738123561392
FOSL2#2355411.28680040304110.0001656657722157630.0020374431917619
FOXA1#316959.234516457821213.31890114386024e-050.000659856684872682
GABPB1#255344.711789224121450.004730054311555960.0222874866792057
GATA2#262436.3724658667770.008058821308742550.0318869194417035
GTF2B#2959315.97191496716210.0005711653715892990.00486676513367176
GTF2F1#2962510.61638406396471.66999681725408e-050.000385102224767497
HDAC2#306648.94374682441750.0004094079565307180.00390235991349015
HEY1#2346264.040111043105710.0002298968555807510.00253058576096101
HMGN3#932456.815456436125490.0001472107253583660.0018997332195357
HNF4A#3172623.13229036295376.51490260560877e-095.12742963999378e-07
IRF1#365956.364303127969920.000205667514205090.00243976709632728
MAX#414944.301703672671410.006644923910676370.028294907991484
MEF2A#420539.371615454822030.002687399947103910.0148001140622013
MXI1#460146.64104775250620.001288516958039140.00863800132105074
MYC#460965.22228187160944.92821127172503e-050.000853702864501063
NFKB1#479065.488063424193843.65870229532191e-050.000707089579979876
NR2C2#7182210.87153696841360.01298583020012040.0460800190360961
PAX5#507955.557971275981520.0003977176196612860.00388597908876462
POLR2A#543062.147453176558070.01019570676818780.0380079033110639
POLR3G#106221362.4058823529410.002756203817184890.0151144746895759
POU2F2#545269.106124057742521.75272139021506e-066.59886334796937e-05
RDBP#7936251.21280133000830.0006240180493507170.00513770761183599
REST#597846.433352477418680.001454954223032070.00932404516777606
RFX5#599348.03194055146340.0006204615428381410.00511003730561254
RXRA#6256516.72884761594441.76223204684013e-066.62511708927057e-05
SETDB1#9869320.16001308900520.0002882529826133590.00306348359124419
SIN3A#2594265.408884726815143.99207083571449e-050.000742657438566415
SIX5#14791238.54335767772950.003504759488012430.0177962648856734
SMARCB1#659839.126357890578710.002900247150367020.0156755634289283
SP1#666765.69838137814092.91961319085282e-050.000609477277712329
STAT2#6773221.75459039548020.003379142399893220.0172548894099862
TAF1#687263.343046285745290.0007162474284635620.00572860814682999
TAF7#687935.716534702461960.01092729379889660.0402098385266352
TBP#690853.088975572580320.006645448275786930.028284455639209
TCF12#693858.862054085155354.06365504449859e-050.000743394761240827
TCF7L2#693435.385088281568670.01290488779931040.046402946354697
TFAP2C#702247.206152406573480.0009421413689212550.00681792561174938
THAP1#55145210.45638153428380.01399147851103650.0491178495534167
TRIM28#10155412.39368336350830.0001149534924635960.00157265231849692
USF1#739155.30124939767330.0005003327549858890.00441150296310437
YY1#752854.092642291544880.001743365462849530.0107241928127307
ZBTB33#10009210.55490834332710.01374250737140590.0483836882201408
ZBTB7A#5134144.901272871917260.004079628118843750.0194856069287443
ZEB1#693538.444216008771930.003623843810733590.0183367550266088
ZNF143#770236.750438276113950.006850259204468580.0290366581864318
ZNF263#1012745.481227758007120.002675609380607230.0147437328180889



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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