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Coexpression cluster:C3956: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=0.699513,0.14394,0.690871,0.855819,0.641468,0.853988,0.937929,0.494933,1.23181,0.221898,0.820209,0.985163,0.436625,0.925331,0.639839,0.667627,1.17594,0.575162,0.452865,0.305559,0.69094,0.242883,1.96998,0.635379,0.743951,1.00973,0.409304,0.842925,0.645155,0.388328,0.795576,1.21459,0.534793,0.439574,0.599922,0.137917,0.596053,0.855276,0.567465,3.05174,0.598234,0.777097,0.259059,0.63803,0.461452,0.726632,0.939121,0.808003,0.247669,0.645308,1.02504,2.18821,0.336258,1.29475,1.45259,0.928548,0.650353,0.892517,0.388177,0.891404,1.25741,0.941709,0.492369,1.14672,2.20718,1.11026,1.54311,1.91674,1.2037,1.75271,1.7986,0.502203,0.333216,1.45054,1.92922,0.414196,0.396746,1.12884,1.20029,0.73687,0.459024,1.14559,0.960908,0.498519,3.09034,0.169933,2.26789,0.381882,1.053,2.0169,1.63834,1.36973,1.23218,0.543775,0.642354,0.560075,0.450952,1.27663,1.05794,0.360456,0.569121,1.22626,1.27082,1.1798,1.09802,3.17067,2.61709,0.921547,0.743661,0.622396,0.703975,1.26794,0.684398,0.830777,1.58942,0.594137,0.188952,0.794219,1.10778,0.547323,1.44203,1.0504,0.850918,0.973172,1.70203,1.12965,2.14531,1.2374,1.48578,0.561252,1.37044,1.87432,1.50051,0.969553,1.65144,1.73097,0.788803,0.843556,1.60823,2.47382,2.06967,1.57016,0.932872,1.27296,1.09989,0.883164,1.08214,2.31409,0.773313,1.33389,3.23473,1.99724,1.37083,0.481626,0.941179,1.78371,1.03563,0.624795,0.744018,0.710709,1.56892,1.35169,1.19946,0.714443,1.11698,0.960047,0.524529,0.936473,0.951408
|tfbs_overrepresentation_for_novel_motifs=0.699513,0.14394,0.690871,0.855819,0.641468,0.853988,0.937929,0.494933,1.23181,0.221898,0.820209,0.985163,0.436625,0.925331,0.639839,0.667627,1.17594,0.575162,0.452865,0.305559,0.69094,0.242883,1.96998,0.635379,0.743951,1.00973,0.409304,0.842925,0.645155,0.388328,0.795576,1.21459,0.534793,0.439574,0.599922,0.137917,0.596053,0.855276,0.567465,3.05174,0.598234,0.777097,0.259059,0.63803,0.461452,0.726632,0.939121,0.808003,0.247669,0.645308,1.02504,2.18821,0.336258,1.29475,1.45259,0.928548,0.650353,0.892517,0.388177,0.891404,1.25741,0.941709,0.492369,1.14672,2.20718,1.11026,1.54311,1.91674,1.2037,1.75271,1.7986,0.502203,0.333216,1.45054,1.92922,0.414196,0.396746,1.12884,1.20029,0.73687,0.459024,1.14559,0.960908,0.498519,3.09034,0.169933,2.26789,0.381882,1.053,2.0169,1.63834,1.36973,1.23218,0.543775,0.642354,0.560075,0.450952,1.27663,1.05794,0.360456,0.569121,1.22626,1.27082,1.1798,1.09802,3.17067,2.61709,0.921547,0.743661,0.622396,0.703975,1.26794,0.684398,0.830777,1.58942,0.594137,0.188952,0.794219,1.10778,0.547323,1.44203,1.0504,0.850918,0.973172,1.70203,1.12965,2.14531,1.2374,1.48578,0.561252,1.37044,1.87432,1.50051,0.969553,1.65144,1.73097,0.788803,0.843556,1.60823,2.47382,2.06967,1.57016,0.932872,1.27296,1.09989,0.883164,1.08214,2.31409,0.773313,1.33389,3.23473,1.99724,1.37083,0.481626,0.941179,1.78371,1.03563,0.624795,0.744018,0.710709,1.56892,1.35169,1.19946,0.714443,1.11698,0.960047,0.524529,0.936473,0.951408
|tfbs_overrepresentation_jaspar=MA0003.1;0.178364,MA0004.1;0.826076,MA0006.1;1.5435,MA0007.1;0.804807,MA0009.1;1.3275,MA0014.1;0.118426,MA0017.1;0.686276,MA0019.1;0.990656,MA0024.1;4.40988,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;0.341392,MA0050.1;0.81185,MA0051.1;0.936307,MA0052.1;1.24796,MA0055.1;0.190716,MA0056.1;0,MA0057.1;2.4146,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;1.04561,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;0.734647,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;0.257905,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;0.560723,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;0.273764,MA0146.1;0.348055,MA0147.1;2.37462,MA0148.1;0.854239,MA0149.1;0.884158,MA0062.2;0.449458,MA0035.2;0.894194,MA0039.2;0.0526989,MA0138.2;1.04628,MA0002.2;0.476938,MA0137.2;0.666381,MA0104.2;2.13189,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;0.312019,MA0155.1;0.711948,MA0156.1;0.669101,MA0157.1;1.09377,MA0158.1;0,MA0159.1;0.565904,MA0160.1;0.871361,MA0161.1;0,MA0162.1;1.43223,MA0163.1;0.122425,MA0164.1;1.01792,MA0080.2;0.643061,MA0018.2;0.987913,MA0099.2;0.902716,MA0079.2;0.69213,MA0102.2;1.88331,MA0258.1;0.519674,MA0259.1;1.40979,MA0442.1;0
}}
}}

Revision as of 21:43, 22 January 2013


Full id: C3956_Mast_cord_Hodgkin_granulocyte_rhabdomyosarcoma_lymphoma_acute



Phase1 CAGE Peaks

Hg19::chr1:24306768..24306779,-p3@SRSF10
Hg19::chr1:24306809..24306828,-p1@SRSF10
Hg19::chr1:24306835..24306868,-p2@SRSF10


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>disease_data<br>

Cell Type
Ontology termp-valuen
hematopoietic stem cell4.85e-34168
angioblastic mesenchymal cell4.85e-34168
hematopoietic cell1.02e-31177
hematopoietic oligopotent progenitor cell9.01e-31161
hematopoietic multipotent progenitor cell9.01e-31161
nucleate cell1.83e-2455
lymphocyte2.39e-2353
common lymphoid progenitor2.39e-2353
lymphoid lineage restricted progenitor cell1.01e-2252
leukocyte2.23e-21136
hematopoietic lineage restricted progenitor cell1.45e-19120
nongranular leukocyte7.19e-19115
lymphocyte of B lineage2.74e-1124
pro-B cell2.74e-1124
T cell2.92e-1125
pro-T cell2.92e-1125
myeloid cell9.68e-11108
common myeloid progenitor9.68e-11108
motile cell1.94e-09386
mature alpha-beta T cell8.33e-0918
alpha-beta T cell8.33e-0918
immature T cell8.33e-0918
mature T cell8.33e-0918
immature alpha-beta T cell8.33e-0918
mesenchymal cell4.23e-08354
B cell7.90e-0814
Uber Anatomy
Ontology termp-valuen
connective tissue1.59e-07371
Disease
Ontology termp-valuen
cancer2.47e-27235
disease of cellular proliferation2.44e-25239
hematologic cancer2.23e-1951
immune system cancer2.23e-1951
organ system cancer3.21e-18137
leukemia5.04e-1639
cell type cancer7.06e-12143
myeloid leukemia7.50e-1231
carcinoma3.05e-11106


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)
MA0003.10.178364
MA0004.10.826076
MA0006.11.5435
MA0007.10.804807
MA0009.11.3275
MA0014.10.118426
MA0017.10.686276
MA0019.10.990656
MA0024.14.40988
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
MA0048.10.341392
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.10.190716
MA0056.10
MA0057.12.4146
MA0058.10.716037
MA0059.10.714521
MA0060.10.492218
MA0061.10.456531
MA0063.10
MA0066.10.941452
MA0067.11.65513
MA0068.11.04561
MA0069.11.31207
MA0070.11.30033
MA0071.10.897953
MA0072.11.29561
MA0073.10.0185922
MA0074.10.935474
MA0076.10.734647
MA0077.11.28751
MA0078.11.04495
MA0081.10.714712
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.10.257905
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
MA0116.10.560723
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
MA0145.10.273764
MA0146.10.348055
MA0147.12.37462
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.20.0526989
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.22.13189
MA0047.20.973066
MA0112.20.264678
MA0065.20.277623
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.10.312019
MA0155.10.711948
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.11.43223
MA0163.10.122425
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.20.69213
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
BCL3#602223.03140186915890.002464674760842910.0138547912884263
BRCA1#672320.18423064322380.0001215704860271640.00164273515204955
CCNT2#90536.336201576962630.003930750035764890.019018048873587
CEBPB#105137.971147625824820.001974187055288560.011528214809465
CHD2#1106310.34402283411690.0009033701102746880.00660740044449739
CTCF#1066435.360256373075030.0064925092527670.0279674643782113
CTCFL#140690319.74647435897440.0001298372005551160.00171863971974345
E2F1#186934.907389214879320.008460985347239390.032561605449198
E2F4#1874312.66806031528440.0004917987006298980.00437503956516916
E2F6#187635.017155731697390.00791769806886330.0322510323172392
EGR1#195834.988179094810140.008056488137383440.0320880010899317
ELF1#199734.258097958807540.01295179875054610.0462689553517456
ETS1#211339.728760922202340.001085840092584840.00762841742428816
GTF2B#2959331.94382993432423.06634405746243e-050.000628302740861917
GTF2F1#2962312.73966087675770.0004835525047438590.00434311489877399
HMGN3#932438.178547723350590.001827766942164210.0108781713968936
IRF1#365937.63716375356390.002244692747297240.0128175760434651
JUN#3725312.51282919233630.0005103313992726250.00444524612248821
MAX#414936.452555509007120.003721913834265510.0186710677235629
MEF2A#4205318.74323090964410.0001518243905622470.00195059509483706
MXI1#460139.96157162875930.001011470541259020.00720727105536952
MYC#460935.22228187160940.007020843755740150.0294761979822217
NANOG#79923329.24477848101273.99627955670032e-050.000738050292877498
NFKB1#479035.488063424193840.006049381815655430.0269788789582901
NFYB#4801316.75979325353650.0002123649923296180.00245998086001697
NRF1#4899312.21027944771090.0005492172401020010.00471397923561907
PAX5#507936.669565531177830.003370290999677260.0173035995337378
POU2F2#545239.106124057742520.001324165192682130.00882881055659659
RAD21#5885310.35503389545630.0009004912073565420.00664544949159906
SETDB1#9869340.32002617801051.52461559299059e-050.000359028924275861
SIN3A#2594235.408884726815140.006318961977991520.0277043814289684
SMARCB1#6598318.25271578115740.000164397760679890.00203237899238246
SP1#666735.69838137814090.005403962701712170.0246747020768643
SPI1#668838.204323508522730.001810593189410520.010912773667408
SRF#6722313.79717826216780.0003806615025800190.00375303565259649
STAT2#6773365.26377118644073.59360517547754e-060.000118395120164574
TAF7#6879311.43306940492390.0006690181981945830.00543494023033946
TAL1#6886329.86861667744023.75103522793067e-050.000720136706194579
TRIM28#10155318.59052504526250.0001555969297255280.00197189512724237
USF1#739136.361499277207960.00388404057290560.0190425928736122
YY1#752834.911170749853860.008441455341808260.0329699758580072
ZBTB33#10009331.66472502998123.14815888737575e-050.000633996463630228
ZNF263#1012738.221841637010680.001799043925565870.010951873894974



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:C3956&oldid=2572467"