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Coexpression cluster:C4046: Difference between revisions

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{{Coexpression_clusters
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,0.259632,0.30793,0.0173907,0.159884,0.257294,0.150733,0.217112,0.123917,0.184317,0.185335,0.0723291,0.258496,0.261744,0.203781,0.21382,0.207559,0.000532415,0.193031,0.00316602,0.115972,0.224568,0.246105,0.173026,0.200432,0.000508432,0.197112,0.240478,0.156465,0.13108,0.256963,0.222798,0.172134,0.176789,0.0969345,0.202137,0.310405,0.280943,0.218161,0.0822373,0.202065,0.106739,0.0536053,0.0537737,0.15113,0.078016,0.0407233,0.0537355,0.319922,0.261724,0.211332,0.187731,0.233626,0.189559,0.0812887,0.0981146,0.064145,0.121913,0.0638699,0.104603,0.0663259,0.0762523,0.128736,0.109171,0.04411,5.26612e-05,0.089609,3.70325e-12,0.13497,0.204393,0.295769,0.286691,0.347036,0.141729,0.263159,0.255956,0.200105,0.227491,0.29837,0.253509,0.177664,0.28365,0.264413,0.131761,0.160658,0.206239,0.19924,0.28689,0.236464,0.325148,0.115817,0.0257187,0.223831,0.11528,0.194982,0.190993,0.281727,0.000393044,0.249955,0.164638,0.224257,0.0935776,0.327622,0.225752,0.207791,0.0958756,0.0859274,0.316866,0.171683,0.0133429,0.271275,0.071111,0.270604,0.101021,0.222548,0.0164735,0.157274,0.215705,0.252796,0.205954,0.361435|tfbs_overrepresentation_for_novel_motifs=0.699513,0.14394,0.690871,0.855819,0.641468,0.853988,2.1595,0.494933,0.491742,1.84557,1.91835,0.985163,2.90305,0.925331,0.639839,0.667627,1.17594,0.575162,0.452865,0.824321,0.69094,0.680949,0.845342,0.635379,2.94706,1.00973,0.409304,0.842925,0.645155,1.00813,0.795576,1.21459,1.3235,0.439574,3.63468,0.137917,0.596053,0.855276,0.567465,0.469078,0.598234,0.777097,1.32383,0.63803,0.151453,0.726632,0.939121,0.808003,0.247669,0.645308,1.02504,0.951993,0.336258,1.29475,1.45259,0.928548,0.650353,0.892517,0.388177,0.891404,1.25741,0.941709,0.492369,2.58389,0.961293,1.11026,1.54311,1.91674,1.2037,1.75271,0.762094,1.25415,0.333216,1.45054,0.430728,2.79908,0.396746,1.12884,1.20029,0.73687,0.459024,1.14559,0.960908,0.498519,1.39759,0.507157,0.303648,0.381882,2.39382,2.0169,1.63834,1.36973,1.23218,0.543775,0.642354,1.37703,0.450952,1.27663,1.05794,0.360456,0.569121,1.22626,1.27082,1.1798,1.09802,0.815119,1.16312,0.921547,0.743661,2.55998,1.67826,1.26794,0.684398,0.830777,1.58942,0.594137,0.188952,0.794219,1.10778,0.547323,1.44203,1.0504,0.850918,2.2314,1.70203,4.14226,0.930979,1.2374,1.48578,0.561252,1.37044,0.798812,1.50051,0.969553,1.65144,0.372828,0.788803,0.843556,1.60823,2.47382,2.06967,1.57016,0.932872,1.27296,1.09989,0.883164,1.08214,2.31409,0.773313,0.539692,0.318511,0.698641,1.37083,0.481626,0.941179,1.78371,1.03563,0.624795,0.744018,4.11334,1.56892,1.35169,1.19946,0.714443,1.11698,0.960047,0.524529,0.936473,0.56135|tfbs_overrepresentation_jaspar=MA0003.1;1.54338,MA0004.1;0.826076,MA0006.1;0.639288,MA0007.1;0.804807,MA0009.1;1.3275,MA0014.1;0.377374,MA0017.1;0.686276,MA0019.1;0.990656,MA0024.1;1.21731,MA0025.1;1.46617,MA0027.1;2.95767,MA0028.1;0.658629,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;2.45333,MA0050.1;0.81185,MA0051.1;0.936307,MA0052.1;1.24796,MA0055.1;7.8496,MA0056.1;0,MA0057.1;0.333427,MA0058.1;0.716037,MA0059.1;0.714521,MA0060.1;0.492218,MA0061.1;0.456531,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;0.0185922,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;2.84236,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;1.80901,MA0113.1;1.00436,MA0114.1;0.549955,MA0115.1;1.57693,MA0116.1;1.3784,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;0.531867,MA0145.1;1.37817,MA0146.1;0.707589,MA0147.1;0.565108,MA0148.1;0.854239,MA0149.1;0.884158,MA0062.2;1.141,MA0035.2;0.894194,MA0039.2;3.37171,MA0138.2;1.04628,MA0002.2;0.476938,MA0137.2;0.666381,MA0104.2;0.491226,MA0047.2;0.973066,MA0112.2;0.731309,MA0065.2;0.277623,MA0150.1;0.744617,MA0151.1;0,MA0152.1;0.902317,MA0153.1;1.43021,MA0154.1;2.30945,MA0155.1;0.256269,MA0156.1;0.669101,MA0157.1;1.09377,MA0158.1;0,MA0159.1;0.565904,MA0160.1;0.871361,MA0161.1;0,MA0162.1;0.149099,MA0163.1;1.2663,MA0164.1;1.01792,MA0080.2;0.643061,MA0018.2;0.987913,MA0099.2;0.902716,MA0079.2;0.0107199,MA0102.2;1.88331,MA0258.1;0.519674,MA0259.1;2.40872,MA0442.1;0}}
|full_id=C4046_breast_Mast_MCF7_lymphoma_CD19_migratory_lung
|id=C4046
}}

Latest revision as of 12:38, 17 September 2013


Full id: C4046_breast_Mast_MCF7_lymphoma_CD19_migratory_lung



Phase1 CAGE Peaks

Hg19::chr20:46130602..46130613,+p3@NCOA3
Hg19::chr20:46130619..46130664,+p1@NCOA3
Hg19::chr20:46130672..46130686,+p2@NCOA3


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
leukocyte1.54e-36136
nongranular leukocyte2.57e-28115
hematopoietic lineage restricted progenitor cell6.69e-28120
hematopoietic stem cell8.09e-22168
angioblastic mesenchymal cell8.09e-22168
myeloid leukocyte1.71e-2172
hematopoietic oligopotent progenitor cell4.83e-20161
hematopoietic multipotent progenitor cell4.83e-20161
classical monocyte9.50e-2042
CD14-positive, CD16-negative classical monocyte9.50e-2042
granulocyte monocyte progenitor cell1.09e-1967
hematopoietic cell3.26e-18177
defensive cell7.67e-1848
phagocyte7.67e-1848
macrophage dendritic cell progenitor1.54e-1761
myeloid lineage restricted progenitor cell3.95e-1766
monopoietic cell5.06e-1759
monocyte5.06e-1759
monoblast5.06e-1759
promonocyte5.06e-1759
lymphocyte of B lineage3.40e-1224
pro-B cell3.40e-1224
lymphoid lineage restricted progenitor cell2.11e-1052
lymphocyte2.11e-1053
common lymphoid progenitor2.11e-1053
myeloid cell2.95e-10108
common myeloid progenitor2.95e-10108
nucleate cell4.04e-0955
B cell7.41e-0914
mesenchymal cell8.27e-09354
connective tissue cell9.63e-08361
Uber Anatomy
Ontology termp-valuen
hematopoietic system1.02e-1998
blood island1.02e-1998
hemolymphoid system8.73e-18108
bone element4.13e-1682
bone marrow1.40e-1576
immune system2.45e-1593
skeletal element8.32e-1490
skeletal system1.72e-11100
connective tissue2.36e-07371


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)
MA0003.11.54338
MA0004.10.826076
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.10.377374
MA0017.10.686276
MA0019.10.990656
MA0024.11.21731
MA0025.11.46617
MA0027.12.95767
MA0028.10.658629
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
MA0048.12.45333
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.17.8496
MA0056.10
MA0057.10.333427
MA0058.10.716037
MA0059.10.714521
MA0060.10.492218
MA0061.10.456531
MA0063.10
MA0066.10.941452
MA0067.11.65513
MA0068.10.405474
MA0069.11.31207
MA0070.11.30033
MA0071.10.897953
MA0072.11.29561
MA0073.10.0185922
MA0074.10.935474
MA0076.11.74184
MA0077.11.28751
MA0078.11.04495
MA0081.10.714712
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.12.84236
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
MA0111.11.80901
MA0113.11.00436
MA0114.10.549955
MA0115.11.57693
MA0116.11.3784
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
MA0144.10.531867
MA0145.11.37817
MA0146.10.707589
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.21.141
MA0035.20.894194
MA0039.23.37171
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.20.491226
MA0047.20.973066
MA0112.20.731309
MA0065.20.277623
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.12.30945
MA0155.10.256269
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.10.149099
MA0163.11.2663
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.20.0107199
MA0102.21.88331
MA0258.10.519674
MA0259.12.40872
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-050.00129729769886249
BCLAF1#9774321.65264761012189.8473954032885e-050.00139300030952736
CCNT2#90536.336201576962630.003930750035764890.0190312736074011
CEBPB#105137.971147625824820.001974187055288560.0115372459217325
CHD2#1106310.34402283411690.0009033701102746880.00661110440382441
CTBP2#1488362.71700033932814.049570681927e-060.000129973298232874
CTCF#1066435.360256373075030.0064925092527670.0279870882388036
CTCFL#140690319.74647435897440.0001298372005551160.00171994766473564
E2F1#186934.907389214879320.008460985347239390.0325904274057806
E2F6#187635.017155731697390.00791769806886330.0322825090226045
EBF1#187938.9064668465690.00141523283560980.0091594163796401
EGR1#195834.988179094810140.008056488137383440.0321149452129843
ELF1#199734.258097958807540.01295179875054610.0463022150239023
ELK4#2005316.2356816584680.0002336043955745990.00255898987512225
EP300#203336.77394172622320.003216880500103790.0167682063560761
ETS1#211339.728760922202340.001085840092584840.00763303852927695
FOSL2#2355316.93020060456170.0002060162053171620.00243340041473864
GABPB1#255337.067683836182170.002832212825417420.0154340451486444
GATA2#2624312.7449317335540.0004829527704283790.00437307997145565
GTF2F1#2962312.73966087675770.0004835525047438590.00434610499508984
HDAC2#3066313.41562023662630.0004140761399857210.00391718278840296
HMGN3#932438.178547723350590.001827766942164210.0108849946782624
HNF4A#3172323.13229036295378.07584663437677e-050.00122913632563054
HNF4G#3174328.75342252644684.20470658818262e-050.000757521737731939
IRF1#365937.63716375356390.002244692747297240.0128280966257169
JUND#372736.994663941871030.002921845042734990.0157004823224017
MAX#414936.452555509007120.003721913834265510.0186836317681738
MEF2A#4205318.74323090964410.0001518243905622470.00195107512316113
MXI1#460139.96157162875930.001011470541259020.00720973053907664
MYC#460935.22228187160940.007020843755740150.0294939825833935
NFKB1#479035.488063424193840.006049381815655430.0269927107342236
NR3C1#2908314.9730233311730.0002978331194675480.00309229477722152
PAX5#507936.669565531177830.003370290999677260.0173138131684847
POU2F2#545239.106124057742520.001324165192682130.00883162964164563
RAD21#5885310.35503389545630.0009004912073565420.00664920822999928
SIN3A#2594235.408884726815140.006318961977991520.0277230023112563
SIX5#147912317.0867153554590.0002004060546325010.00239915267535119
SMC3#9126315.04493284493280.0002935825420371870.00309461718892024
SP1#666735.69838137814090.005403962701712170.0246919744762706
TAF7#6879311.43306940492390.0006690181981945830.0054391710728043
TCF12#6938310.63446490218640.0008313523990202070.00629992839945373
TCF7L2#6934310.77017656313730.0008003181298398380.00614591361487815
USF1#739136.361499277207960.00388404057290560.0190604883654585
YY1#752834.911170749853860.008441455341808260.0329835442569162
ZBTB7A#5134137.35190930787590.002516255860282270.01404345886774
ZNF143#7702313.50087655222790.0004062804962997170.00389601769837904



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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