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Coexpression cluster:C4393: Difference between revisions

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{{Coexpression_clusters
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kinase activity!0.00571058518780172!1633$GO:0006288!base-excision repair, DNA ligation!0.0085656256290494!3148$GO:0051103!DNA ligation during DNA repair!0.00951708164044024!3148$GO:0019136!deoxynucleoside kinase activity!0.00999264154436685!1633$GO:0006266!DNA ligation!0.0102764813809805!3148$GO:0008301!DNA bending activity!0.0102764813809805!3148$GO:0019206!nucleoside kinase activity!0.0102764813809805!1633$GO:0006268!DNA unwinding during replication!0.0102764813809805!3148$GO:0032392!DNA geometric change!0.0102764813809805!3148$GO:0032508!DNA duplex unwinding!0.0102764813809805!3148$GO:0006284!base-excision repair!0.0181609510018751!3148$GO:0000793!condensed chromosome!0.0247272939016887!3148$GO:0003697!single-stranded DNA binding!0.0260813256323868!3148$GO:0048471!perinuclear region of cytoplasm!0.0260813256323868!3148$GO:0006220!pyrimidine nucleotide metabolic process!0.0262424007472481!1633$GO:0019205!nucleobase, nucleoside, nucleotide kinase activity!0.0324359297091708!1633$GO:0000228!nuclear chromosome!0.0332077924654081!3148$GO:0003690!double-stranded DNA binding!0.0342095504590265!3148$GO:0048015!phosphoinositide-mediated signaling!0.0386988232117492!3148$GO:0043566!structure-specific DNA binding!0.0447605780502602!3148$GO:0006261!DNA-dependent DNA replication!0.0447605780502602!3148$GO:0006334!nucleosome 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941,0.120196,0.0986735,0.108462,0.0595618,0.21593,0.158479,0.220319,0.195218,0.124213,0.259632,0.30793,0.180606,0.159884,0.257294,0.150733,0.217112,0.123917,0.184317,0.185335,0.0723291,0.258496,0.261744,0.203781,0.21382,0.207559,0.141867,0.193031,0.249101,0.115972,0.224568,0.246105,0.173026,0.200432,0.139785,0.197112,0.240478,0.156465,0.13108,0.256963,0.222798,0.172134,0.176789,0.0969345,0.202137,0.310405,0.280943,0.218161,0.0822373,0.202065,0.106739,0.0536053,0.0537737,0.15113,0.078016,0.0407233,0.0537355,0.319922,0.261724,0.211332,0.187731,0.233626,0.189559,0.0812887,0.0981146,0.064145,0.121913,0.0638699,0.104603,0.0663259,0.0762523,0.128736,0.109171,0.04411,0.066952,0.089609,0.0367455,0.13497,0.204393,0.295769,0.286691,0.347036,0.141729,0.263159,0.255956,0.200105,0.227491,0.29837,0.253509,0.177664,0.28365,0.264413,0.131761,0.160658,0.206239,0.19924,0.28689,0.236464,0.325148,0.115817,0.218052,0.223831,0.11528,0.194982,0.190993,0.281727,0.283218,0.249955,0.164638,0.224257,0.0935776,0.327622,0.225752,0.207791,0.0958756,0.0859274,0.316866,0.171683,0.158847,0.271275,0.071111,0.270604,0.101021,0.222548,0.175934,0.157274,0.215705,0.252796,0.205954,0.361435|tfbs_overrepresentation_for_novel_motifs=0.699513,2.0185,0.690871,0.855819,0.641468,0.853988,0.937929,0.494933,0.491742,1.18351,0.820209,0.985163,0.436625,0.925331,0.639839,0.667627,1.17594,0.575162,0.452865,0.305559,0.69094,0.680949,0.845342,0.635379,0.743951,1.00973,0.409304,0.842925,1.55576,0.388328,0.795576,1.21459,0.534793,0.439574,0.599922,1.36391,3.61775,0.855276,0.567465,1.18324,0.598234,0.777097,0.259059,0.63803,0.461452,0.726632,0.939121,0.808003,0.247669,0.645308,1.02504,0.951993,0.336258,1.29475,1.45259,0.928548,0.650353,0.892517,1.0078,0.891404,1.25741,0.941709,0.492369,1.14672,0.961293,1.11026,1.54311,1.91674,1.2037,1.75271,1.7986,0.502203,2.41357,1.45054,1.10051,0.414196,0.396746,1.12884,1.20029,0.73687,0.459024,2.58159,0.960908,0.498519,1.39759,2.22068,0.82001,0.381882,1.053,2.0169,1.63834,1.36973,1.23218,0.543775,0.642354,0.560075,0.450952,1.27663,1.05794,0.360456,0.569121,1.22626,1.27082,1.1798,1.09802,0.815119,1.16312,0.921547,0.743661,0.622396,0.703975,1.26794,0.684398,0.830777,1.58942,0.594137,0.553386,0.794219,1.10778,0.547323,1.44203,1.0504,0.850918,0.973172,1.70203,1.12965,0.930979,1.2374,1.48578,0.561252,1.37044,0.798812,1.50051,0.969553,1.65144,0.372828,0.788803,0.843556,1.60823,2.47382,2.06967,1.57016,0.932872,1.27296,1.09989,0.883164,1.08214,2.31409,0.773313,0.539692,0.318511,1.99724,1.37083,1.21015,0.941179,1.78371,1.03563,0.624795,0.744018,0.710709,1.56892,1.35169,1.19946,0.714443,1.11698,0.960047,0.524529,0.936473,0.56135|tfbs_overrepresentation_jaspar=MA0003.1;3.22681,MA0004.1;1.93041,MA0006.1;1.5435,MA0007.1;0.804807,MA0009.1;1.3275,MA0014.1;2.44638,MA0017.1;0.686276,MA0019.1;0.990656,MA0024.1;2.72668,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;0.904546,MA0050.1;1.90116,MA0051.1;0.936307,MA0052.1;1.24796,MA0055.1;0.190716,MA0056.1;0,MA0057.1;0.886807,MA0058.1;1.70328,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;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;0.715722,MA0089.1;0,MA0090.1;0.751469,MA0091.1;0.829044,MA0092.1;1.84783,MA0093.1;2.626,MA0095.1;0,MA0098.1;0,MA0100.1;0.956299,MA0101.1;0.646932,MA0103.1;0.628063,MA0105.1;1.5295,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;2.32521,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;1.12079,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;1.70974,MA0147.1;1.38767,MA0148.1;0.854239,MA0149.1;0.884158,MA0062.2;0.449458,MA0035.2;0.894194,MA0039.2;1.15986,MA0138.2;1.04628,MA0002.2;0.476938,MA0137.2;0.666381,MA0104.2;1.2307,MA0047.2;0.973066,MA0112.2;0.264678,MA0065.2;1.39232,MA0150.1;1.76247,MA0151.1;0,MA0152.1;0.902317,MA0153.1;1.43021,MA0154.1;0.312019,MA0155.1;1.31345,MA0156.1;0.669101,MA0157.1;1.09377,MA0158.1;0,MA0159.1;1.38935,MA0160.1;0.871361,MA0161.1;0,MA0162.1;1.43223,MA0163.1;3.96434,MA0164.1;1.01792,MA0080.2;0.643061,MA0018.2;0.987913,MA0099.2;0.902716,MA0079.2;3.61229,MA0102.2;1.88331,MA0258.1;0.519674,MA0259.1;0.575594,MA0442.1;0}}
|full_id=C4393_Reticulocytes_Burkitt_Dendritic_non_lymphoma_acute_NK
|gostat_on_coexpression_clusters=GO:0004137!deoxycytidine kinase activity!0.00571058518780172!1633$GO:0006288!base-excision repair, DNA ligation!0.0085656256290494!3148$GO:0051103!DNA ligation during DNA repair!0.00951708164044024!3148$GO:0019136!deoxynucleoside kinase activity!0.00999264154436685!1633$GO:0006266!DNA ligation!0.0102764813809805!3148$GO:0008301!DNA bending activity!0.0102764813809805!3148$GO:0019206!nucleoside kinase activity!0.0102764813809805!1633$GO:0006268!DNA unwinding during replication!0.0102764813809805!3148$GO:0032392!DNA geometric change!0.0102764813809805!3148$GO:0032508!DNA duplex unwinding!0.0102764813809805!3148$GO:0006284!base-excision repair!0.0181609510018751!3148$GO:0000793!condensed chromosome!0.0247272939016887!3148$GO:0003697!single-stranded DNA binding!0.0260813256323868!3148$GO:0048471!perinuclear region of cytoplasm!0.0260813256323868!3148$GO:0006220!pyrimidine nucleotide metabolic process!0.0262424007472481!1633$GO:0019205!nucleobase, nucleoside, nucleotide kinase activity!0.0324359297091708!1633$GO:0000228!nuclear chromosome!0.0332077924654081!3148$GO:0003690!double-stranded DNA binding!0.0342095504590265!3148$GO:0048015!phosphoinositide-mediated signaling!0.0386988232117492!3148$GO:0043566!structure-specific DNA binding!0.0447605780502602!3148$GO:0006261!DNA-dependent DNA replication!0.0447605780502602!3148$GO:0006334!nucleosome assembly!0.0484070896480807!3148
|id=C4393
}}

Latest revision as of 12:45, 17 September 2013


Full id: C4393_Reticulocytes_Burkitt_Dendritic_non_lymphoma_acute_NK



Phase1 CAGE Peaks

Hg19::chr4:174254864..174254925,-p3@HMGB2
Hg19::chr4:71859385..71859407,+p2@DCK
Hg19::chr4:71859413..71859473,+p3@DCK


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

GO IDGO nameFDR corrected p-value
GO:0004137deoxycytidine kinase activity0.00571058518780172
GO:0006288base-excision repair, DNA ligation0.0085656256290494
GO:0051103DNA ligation during DNA repair0.00951708164044024
GO:0019136deoxynucleoside kinase activity0.00999264154436685
GO:0006266DNA ligation0.0102764813809805
GO:0008301DNA bending activity0.0102764813809805
GO:0019206nucleoside kinase activity0.0102764813809805
GO:0006268DNA unwinding during replication0.0102764813809805
GO:0032392DNA geometric change0.0102764813809805
GO:0032508DNA duplex unwinding0.0102764813809805
GO:0006284base-excision repair0.0181609510018751
GO:0000793condensed chromosome0.0247272939016887
GO:0003697single-stranded DNA binding0.0260813256323868
GO:0048471perinuclear region of cytoplasm0.0260813256323868
GO:0006220pyrimidine nucleotide metabolic process0.0262424007472481
GO:0019205nucleobase, nucleoside, nucleotide kinase activity0.0324359297091708
GO:0000228nuclear chromosome0.0332077924654081
GO:0003690double-stranded DNA binding0.0342095504590265
GO:0048015phosphoinositide-mediated signaling0.0386988232117492
GO:0043566structure-specific DNA binding0.0447605780502602
GO:0006261DNA-dependent DNA replication0.0447605780502602
GO:0006334nucleosome assembly0.0484070896480807



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><br>disease_data<br>

Cell Type
Ontology termp-valuen
nucleate cell9.89e-1155
lymphocyte1.08e-0953
common lymphoid progenitor1.08e-0953
lymphoid lineage restricted progenitor cell3.35e-0952
lymphocyte of B lineage1.60e-0824
pro-B cell1.60e-0824
Disease
Ontology termp-valuen
cancer2.03e-25235
disease of cellular proliferation1.45e-24239
hematologic cancer2.55e-2351
immune system cancer2.55e-2351
leukemia7.34e-1939
organ system cancer5.06e-17137
myeloid leukemia2.12e-1431
cell type cancer3.71e-09143
carcinoma1.36e-08106
lymphoma2.59e-0710


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)
MA0003.13.22681
MA0004.11.93041
MA0006.11.5435
MA0007.10.804807
MA0009.11.3275
MA0014.12.44638
MA0017.10.686276
MA0019.10.990656
MA0024.12.72668
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
MA0048.10.904546
MA0050.11.90116
MA0051.10.936307
MA0052.11.24796
MA0055.10.190716
MA0056.10
MA0057.10.886807
MA0058.11.70328
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
MA0076.10.734647
MA0077.11.28751
MA0078.11.04495
MA0081.10.714712
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.10.715722
MA0089.10
MA0090.10.751469
MA0091.10.829044
MA0092.11.84783
MA0093.12.626
MA0095.10
MA0098.10
MA0100.10.956299
MA0101.10.646932
MA0103.10.628063
MA0105.11.5295
MA0106.10.986396
MA0107.10.556367
MA0108.21.15387
MA0109.10
MA0111.10.767139
MA0113.11.00436
MA0114.12.32521
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
MA0139.11.12079
MA0140.10.894983
MA0141.10.712476
MA0142.11.12317
MA0143.11.00455
MA0144.10.531867
MA0145.10.273764
MA0146.11.70974
MA0147.11.38767
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.21.15986
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.21.2307
MA0047.20.973066
MA0112.20.264678
MA0065.21.39232
MA0150.11.76247
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.10.312019
MA0155.11.31345
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.11.38935
MA0160.10.871361
MA0161.10
MA0162.11.43223
MA0163.13.96434
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.23.61229
MA0102.21.88331
MA0258.10.519674
MA0259.10.575594
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#467214.97544968400580.005768294540793880.0259670221356022
BHLHE40#8553229.91454236465160.001467483527106140.00939972475237281
CCNT2#90536.336201576962630.003930750035764890.0190710583938144
E2F1#186934.907389214879320.008460985347239390.0326868701886637
E2F4#1874312.66806031528440.0004917987006298980.00438287946881867
E2F6#187635.017155731697390.00791769806886330.0323671703700491
EGR1#195834.988179094810140.008056488137383440.0321837348753132
RXRA#6256213.38307809275550.007196434429465730.0298355926870299
TFAP2A#7020211.01242291536330.01054990655215560.0390301696918379
ZBTB7A#5134137.35190930787590.002516255860282270.0140667618987271



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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