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Coexpression cluster:C3865: Difference between revisions

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{{Coexpression_clusters
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164638,0.224257,0.0935776,0.327622,0.225752,0.207791,0.0958756,0.0859274,0.316866,0.171683,0.158847,0.271275,0.071111,0.270604,0.101021,0.222548,0.175934,0.157274,0.215705,0.252796,0.205954,0.361435|tfbs_overrepresentation_for_novel_motifs=0.699513,0.869629,0.690871,0.855819,0.641468,0.853988,0.937929,0.494933,0.491742,1.84557,0.820209,0.985163,1.94915,0.925331,0.639839,0.667627,1.17594,0.575162,2.00385,0.305559,0.69094,0.242883,0.845342,0.635379,1.7611,1.00973,0.409304,1.96502,2.63304,0.388328,0.795576,1.21459,0.534793,0.439574,0.599922,0.427404,0.596053,0.855276,0.567465,5.3038,0.598234,0.777097,0.259059,0.63803,1.44641,0.726632,0.939121,0.808003,0.69206,0.645308,1.02504,0.951993,0.336258,1.29475,1.45259,0.928548,0.650353,0.892517,1.78399,0.891404,1.25741,0.941709,0.492369,1.14672,0.961293,1.11026,1.54311,1.91674,1.2037,1.75271,1.7986,0.502203,2.41357,1.45054,1.10051,0.414196,0.396746,1.12884,1.20029,0.73687,0.459024,1.14559,0.960908,0.498519,1.39759,2.22068,2.26789,0.381882,1.053,2.0169,1.63834,1.36973,1.23218,0.543775,0.642354,0.560075,0.450952,1.27663,1.05794,3.495,0.569121,1.22626,1.27082,1.1798,1.09802,3.17067,1.16312,0.921547,0.743661,1.50815,0.703975,1.26794,0.684398,0.830777,1.58942,0.594137,1.05469,0.794219,2.50498,0.547323,1.44203,1.0504,0.850918,0.973172,1.70203,1.12965,0.930979,1.2374,1.48578,2.36206,1.37044,0.798812,1.50051,0.969553,1.65144,0.372828,0.788803,0.843556,1.60823,2.47382,2.06967,1.57016,0.932872,1.27296,1.09989,0.883164,1.08214,2.31409,0.773313,0.539692,0.318511,0.698641,1.37083,0.481626,0.941179,1.78371,1.03563,1.51317,0.744018,0.710709,1.56892,1.35169,1.19946,0.714443,1.11698,0.960047,2.24188,0.936473,2.56478|tfbs_overrepresentation_jaspar=MA0003.1;3.8806,MA0004.1;0.826076,MA0006.1;1.5435,MA0007.1;0.804807,MA0009.1;1.3275,MA0014.1;1.24048,MA0017.1;0.686276,MA0019.1;0.990656,MA0024.1;1.21731,MA0025.1;1.46617,MA0027.1;2.95767,MA0028.1;1.58389,MA0029.1;1.23771,MA0030.1;1.22561,MA0031.1;1.15713,MA0038.1;0.94098,MA0040.1;1.24388,MA0041.1;0.847069,MA0042.1;0.810843,MA0043.1;1.32783,MA0046.1;1.31611,MA0048.1;0.904546,MA0050.1;0.81185,MA0051.1;0.936307,MA0052.1;1.24796,MA0055.1;0.557638,MA0056.1;0,MA0057.1;0.333427,MA0058.1;0.716037,MA0059.1;0.714521,MA0060.1;0.492218,MA0061.1;1.15625,MA0063.1;0,MA0066.1;0.941452,MA0067.1;1.65513,MA0068.1;0.405474,MA0069.1;1.31207,MA0070.1;1.30033,MA0071.1;0.897953,MA0072.1;1.29561,MA0073.1;0.211629,MA0074.1;0.935474,MA0076.1;1.74184,MA0077.1;1.28751,MA0078.1;1.04495,MA0081.1;0.714712,MA0083.1;1.33535,MA0084.1;1.84562,MA0087.1;1.29304,MA0088.1;1.31954,MA0089.1;0,MA0090.1;0.751469,MA0091.1;0.829044,MA0092.1;0.785956,MA0093.1;0.642957,MA0095.1;0,MA0098.1;0,MA0100.1;0.956299,MA0101.1;0.646932,MA0103.1;0.628063,MA0105.1;0.31555,MA0106.1;0.986396,MA0107.1;0.556367,MA0108.2;1.15387,MA0109.1;0,MA0111.1;0.767139,MA0113.1;1.00436,MA0114.1;0.549955,MA0115.1;1.57693,MA0116.1;2.36034,MA0117.1;1.36676,MA0119.1;0.695578,MA0122.1;1.39371,MA0124.1;1.53432,MA0125.1;1.44766,MA0130.1;0,MA0131.1;1.06461,MA0132.1;0,MA0133.1;0,MA0135.1;1.35921,MA0136.1;0.948776,MA0139.1;0.440097,MA0140.1;0.894983,MA0141.1;0.712476,MA0142.1;1.12317,MA0143.1;1.00455,MA0144.1;1.31729,MA0145.1;2.11725,MA0146.1;1.16674,MA0147.1;0.565108,MA0148.1;0.854239,MA0149.1;0.884158,MA0062.2;2.96208,MA0035.2;0.894194,MA0039.2;0.432958,MA0138.2;1.04628,MA0002.2;0.476938,MA0137.2;1.60005,MA0104.2;1.2307,MA0047.2;0.973066,MA0112.2;0.264678,MA0065.2;0.277623,MA0150.1;0.744617,MA0151.1;0,MA0152.1;0.902317,MA0153.1;1.43021,MA0154.1;3.19371,MA0155.1;0.256269,MA0156.1;1.60572,MA0157.1;1.09377,MA0158.1;0,MA0159.1;0.565904,MA0160.1;0.871361,MA0161.1;0,MA0162.1;0.8915,MA0163.1;0.387745,MA0164.1;1.01792,MA0080.2;0.643061,MA0018.2;0.987913,MA0099.2;0.902716,MA0079.2;0.181755,MA0102.2;1.88331,MA0258.1;0.519674,MA0259.1;1.40979,MA0442.1;0}}
|full_id=C3865_melanoma_CD4_anaplastic_choriocarcinoma_teratocarcinoma_lymphangiectasia_CD8
|id=C3865
}}

Latest revision as of 12:34, 17 September 2013


Full id: C3865_melanoma_CD4_anaplastic_choriocarcinoma_teratocarcinoma_lymphangiectasia_CD8



Phase1 CAGE Peaks

Hg19::chr1:151881923..151881943,-p2@THEM4
Hg19::chr1:151881949..151881970,-p3@THEM4
Hg19::chr1:151881977..151882000,-p1@THEM4


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>

Cell Type
Ontology termp-valuen
mature alpha-beta T cell7.94e-1118
alpha-beta T cell7.94e-1118
immature T cell7.94e-1118
mature T cell7.94e-1118
immature alpha-beta T cell7.94e-1118
CD8-positive, alpha-beta T cell1.42e-0711
T cell3.21e-0725
pro-T cell3.21e-0725
Uber Anatomy
Ontology termp-valuen
blood7.96e-0815
haemolymphatic fluid7.96e-0815
organism substance7.96e-0815


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)
MA0003.13.8806
MA0004.10.826076
MA0006.11.5435
MA0007.10.804807
MA0009.11.3275
MA0014.11.24048
MA0017.10.686276
MA0019.10.990656
MA0024.11.21731
MA0025.11.46617
MA0027.12.95767
MA0028.11.58389
MA0029.11.23771
MA0030.11.22561
MA0031.11.15713
MA0038.10.94098
MA0040.11.24388
MA0041.10.847069
MA0042.10.810843
MA0043.11.32783
MA0046.11.31611
MA0048.10.904546
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.10.557638
MA0056.10
MA0057.10.333427
MA0058.10.716037
MA0059.10.714521
MA0060.10.492218
MA0061.11.15625
MA0063.10
MA0066.10.941452
MA0067.11.65513
MA0068.10.405474
MA0069.11.31207
MA0070.11.30033
MA0071.10.897953
MA0072.11.29561
MA0073.10.211629
MA0074.10.935474
MA0076.11.74184
MA0077.11.28751
MA0078.11.04495
MA0081.10.714712
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.11.31954
MA0089.10
MA0090.10.751469
MA0091.10.829044
MA0092.10.785956
MA0093.10.642957
MA0095.10
MA0098.10
MA0100.10.956299
MA0101.10.646932
MA0103.10.628063
MA0105.10.31555
MA0106.10.986396
MA0107.10.556367
MA0108.21.15387
MA0109.10
MA0111.10.767139
MA0113.11.00436
MA0114.10.549955
MA0115.11.57693
MA0116.12.36034
MA0117.11.36676
MA0119.10.695578
MA0122.11.39371
MA0124.11.53432
MA0125.11.44766
MA0130.10
MA0131.11.06461
MA0132.10
MA0133.10
MA0135.11.35921
MA0136.10.948776
MA0139.10.440097
MA0140.10.894983
MA0141.10.712476
MA0142.11.12317
MA0143.11.00455
MA0144.11.31729
MA0145.12.11725
MA0146.11.16674
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.22.96208
MA0035.20.894194
MA0039.20.432958
MA0138.21.04628
MA0002.20.476938
MA0137.21.60005
MA0104.21.2307
MA0047.20.973066
MA0112.20.264678
MA0065.20.277623
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.13.19371
MA0155.10.256269
MA0156.11.60572
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.10.8915
MA0163.10.387745
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.20.181755
MA0102.21.88331
MA0258.10.519674
MA0259.11.40979
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
ATF3#467322.46317452600878.81932387510763e-050.00129656723844646
BCLAF1#9774321.65264761012189.8473954032885e-050.00139224601126851
CCNT2#90536.336201576962630.003930750035764890.019008362410763
CTCF#1066435.360256373075030.0064925092527670.0279501720465677
CTCFL#140690319.74647435897440.0001298372005551160.00171798649294005
E2F1#186934.907389214879320.008460985347239390.0325448161711968
E2F4#1874312.66806031528440.0004917987006298980.00437317705364717
E2F6#187635.017155731697390.00791769806886330.0322309194190058
EBF1#187938.9064668465690.00141523283560980.00915431079637386
EGR1#195834.988179094810140.008056488137383440.032072100803514
ELF1#199734.258097958807540.01295179875054610.0462420658316793
ELK4#2005316.2356816584680.0002336043955745990.00255738044752783
ETS1#211339.728760922202340.001085840092584840.0076243144701807
FOSL2#2355316.93020060456170.0002060162053171620.00243092604983833
FOXA1#3169311.08141974938550.000734755275698670.00581385758305124
GABPB1#255337.067683836182170.002832212825417420.0154163483230192
GATA1#2623313.56030814380040.0004009615963782630.00387956532927084
GATA3#2625327.2365163572064.94721007899563e-050.000851345647454646
GTF2F1#2962312.73966087675770.0004835525047438590.00433938305919779
HMGN3#932438.178547723350590.001827766942164210.0108725950716346
IRF1#365937.63716375356390.002244692747297240.0128112719730574
MAX#414936.452555509007120.003721913834265510.0186567294906098
MXI1#460139.96157162875930.001011470541259020.00720333936982959
MYC#460935.22228187160940.007020843755740150.0294572513661315
NRF1#4899312.21027944771090.0005492172401020010.00471281729841532
PAX5#507936.669565531177830.003370290999677260.0172959472121907
POU2F2#545239.106124057742520.001324165192682130.00882374073620423
REST#597839.650028716128020.001112636247114590.00767774146101094
RFX5#5993312.04791082719510.0005717246050312580.0048462256330541
SIX5#147912317.0867153554590.0002004060546325010.00239777843278311
SMARCB1#6598318.25271578115740.000164397760679890.00203021612009543
SMC3#9126315.04493284493280.0002935825420371870.00309087370038525
SP1#666735.69838137814090.005403962701712170.0246585311343987
SRF#6722313.79717826216780.0003806615025800190.00375161901179151
STAT1#6772320.70658749719920.0001125992441046670.00154876234097818
STAT3#6774310.51946499715420.0008589184530415310.00642721102795762
TCF7L2#6934310.77017656313730.0008003181298398380.0061395934451552
TFAP2A#7020316.5186343730450.0002218033880766340.00248284287752793
TFAP2C#7022310.80922860986020.0007916746575753130.00616062212670502
USF1#739136.361499277207960.00388404057290560.0190318716990564
YY1#752834.911170749853860.008441455341808260.0329490284577162
ZBTB7A#5134137.35190930787590.002516255860282270.0140239738402273
ZNF143#7702313.50087655222790.0004062804962997170.00389137277632484
ZNF263#1012738.221841637010680.001799043925565870.0109448563256349



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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