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Coexpression cluster:C3640: Difference between revisions

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{{Coexpression_clusters
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demethylase activity (H4-R3 specific)!0.0024726245143059!23210$GO:0033746!histone demethylase activity (H3-R2 specific)!0.0024726245143059!23210$GO:0032452!histone demethylase activity!0.00618119735410036!23210$GO:0032451!demethylase activity!0.00618119735410036!23210$GO:0008536!Ran GTPase binding!0.0108779465636226!29107$GO:0006611!protein export from nucleus!0.0115367065479968!29107$GO:0006405!RNA export from nucleus!0.021184878106964!29107$GO:0051168!nuclear export!0.0228100652115979!29107$GO:0017016!Ras GTPase binding!0.0228100652115979!29107$GO:0051213!dioxygenase activity!0.0228100652115979!23210$GO:0016702!oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen!0.0228100652115979!23210$GO:0016701!oxidoreductase activity, acting on single donors with incorporation of molecular oxygen!0.0228100652115979!23210$GO:0031267!small GTPase binding!0.0228100652115979!29107$GO:0005643!nuclear pore!0.0228100652115979!29107$GO:0050658!RNA transport!0.0228100652115979!29107$GO:0051236!establishment of RNA localization!0.0228100652115979!29107$GO:0050657!nucleic acid transport!0.0228100652115979!29107$GO:0006403!RNA localization!0.0228100652115979!29107$GO:0007507!heart development!0.0228100652115979!23210$GO:0051020!GTPase binding!0.0228100652115979!29107$GO:0046930!pore complex!0.0228100652115979!29107$GO:0015931!nucleobase, nucleoside, nucleotide and nucleic acid transport!0.0233421005353548!29107$GO:0044453!nuclear membrane part!0.0238275617848449!29107$GO:0031965!nuclear membrane!0.0292470614675695!29107$GO:0006913!nucleocytoplasmic transport!0.0292470614675695!29107$GO:0051169!nuclear transport!0.0292470614675695!29107$GO:0001568!blood vessel development!0.0292470614675695!23210$GO:0001944!vasculature development!0.0292470614675695!23210$GO:0005635!nuclear envelope!0.032988036057757!29107$GO:0006605!protein targeting!0.0358207019324699!29107$GO:0019899!enzyme 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88263,0.0719199,0.264884,0.162568,0.19104,0.163057,0.219428,0.208013,0.0900729,0.0953646,0.166124,0.252184,0.378361,0.255516,0.20753,0.119514,0.179412,0.193601,0.220904,0.222977,0.0664606,0.310674,0.21801,0.198614,0.186804,0.123324,0.199468,0.0325925,0.0933115,0.12405,0.179889,0.226869,0.27872,0.0855609,0.131118,0.20837,0.247588,0.222339,0.0673329,0.20847,0.0391817,0.113092,0.145701,0.229428,0.162145,0.228955,0.168748,0.0384949,0.0660995,0.0521984,0.0455518,0.268741,0.201602,0.350452,0.154941,0.120196,0.0986735,0.108462,0.0595618,0.21593,0.158479,0.220319,0.195218,0.124213,0.259632,0.0532009,0.180606,0.159884,0.257294,0.150733,0.217112,0.123917,0.184317,0.185335,0.0723291,0.258496,0.261744,0.203781,0.21382,0.207559,0.141867,0.193031,0.249101,0.115972,0.224568,0.246105,0.173026,0.200432,0.139785,0.197112,0.240478,0.156465,0.13108,0.256963,0.222798,0.172134,0.176789,0.0969345,0.202137,0.310405,0.0437875,0.218161,0.0822373,0.202065,0.106739,0.0536053,0.0537737,0.15113,0.078016,0.0407233,0.0537355,0.319922,0.261724,0.211332,0.187731,0.233626,0.189559,0.0812887,0.0981146,0.064145,0.121913,0.0638699,0.104603,0.0663259,0.0762523,0.128736,0.109171,0.04411,0.066952,0.089609,0.0367455,0.13497,0.204393,0.295769,0.286691,0.347036,0.141729,0.263159,0.255956,0.200105,0.0280973,0.29837,0.253509,0.177664,0.28365,0.264413,0.131761,0.160658,0.206239,0.19924,0.0457735,0.236464,0.0597546,0.115817,0.218052,0.223831,0.11528,0.194982,0.190993,0.281727,0.283218,0.249955,0.164638,0.224257,0.0935776,0.327622,0.225752,0.207791,0.0958756,0.0859274,0.316866,0.171683,0.158847,0.0406636,0.071111,0.270604,0.101021,0.222548,0.175934,0.157274,0.215705,0.252796,0.205954,0.0750181|tfbs_overrepresentation_for_novel_motifs=0.699513,0.442617,0.690871,0.855819,0.641468,0.853988,0.937929,0.494933,0.491742,0.63186,0.820209,0.985163,0.436625,0.925331,0.639839,0.667627,1.17594,0.575162,0.452865,0.305559,0.69094,0.680949,0.845342,0.635379,0.743951,1.00973,0.409304,0.842925,0.645155,0.388328,0.795576,1.21459,0.534793,0.439574,0.599922,0.843849,0.596053,0.855276,0.567465,1.18324,0.598234,0.777097,0.259059,0.63803,0.901413,1.72524,0.939121,0.808003,0.247669,0.645308,1.02504,0.951993,0.336258,1.29475,1.45259,0.928548,0.650353,0.892517,0.388177,0.891404,1.25741,0.941709,0.492369,1.14672,0.961293,1.11026,1.54311,1.91674,1.2037,1.75271,0.762094,0.502203,0.886337,1.45054,0.430728,0.414196,0.396746,1.12884,1.20029,0.73687,0.459024,1.14559,0.960908,0.498519,1.39759,0.507157,0.82001,0.381882,1.053,2.0169,1.63834,1.36973,1.23218,0.543775,0.642354,0.560075,0.450952,1.27663,1.05794,0.360456,0.569121,1.22626,1.27082,1.1798,1.09802,0.815119,2.61709,0.921547,0.743661,0.622396,0.703975,1.26794,0.684398,0.830777,1.58942,0.594137,0.553386,0.794219,1.10778,0.547323,1.44203,1.0504,0.850918,0.973172,1.70203,1.12965,0.930979,1.2374,1.48578,0.561252,1.37044,0.798812,1.50051,0.969553,1.65144,0.372828,0.788803,0.843556,1.60823,2.47382,2.06967,1.57016,0.932872,1.27296,1.09989,0.883164,1.08214,2.31409,0.773313,0.539692,0.853445,0.698641,1.37083,0.481626,0.941179,1.78371,1.03563,0.624795,0.744018,0.710709,1.56892,1.35169,1.19946,0.714443,1.11698,0.960047,0.524529,0.936473,0.56135|tfbs_overrepresentation_jaspar=MA0003.1;0.178364,MA0004.1;0.826076,MA0006.1;0.639288,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;0.341392,MA0050.1;0.81185,MA0051.1;0.936307,MA0052.1;1.24796,MA0055.1;0.190716,MA0056.1;0,MA0057.1;0.886807,MA0058.1;0.716037,MA0059.1;1.70014,MA0060.1;0.492218,MA0061.1;0.456531,MA0063.1;0,MA0066.1;2.1667,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;0.668628,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;1.77664,MA0091.1;1.93651,MA0092.1;0.785956,MA0093.1;0.642957,MA0095.1;0,MA0098.1;0,MA0100.1;0.956299,MA0101.1;1.55947,MA0103.1;0.628063,MA0105.1;0.31555,MA0106.1;0.986396,MA0107.1;1.36919,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;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;1.31729,MA0145.1;0.273764,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;2.74132,MA0138.2;1.04628,MA0002.2;0.476938,MA0137.2;1.60005,MA0104.2;1.2307,MA0047.2;0.973066,MA0112.2;0.731309,MA0065.2;0.760954,MA0150.1;0.744617,MA0151.1;0,MA0152.1;0.902317,MA0153.1;1.43021,MA0154.1;1.51687,MA0155.1;0.256269,MA0156.1;0.669101,MA0157.1;1.09377,MA0158.1;0,MA0159.1;0.565904,MA0160.1;2.02335,MA0161.1;0,MA0162.1;0.455568,MA0163.1;0.122425,MA0164.1;1.01792,MA0080.2;0.643061,MA0018.2;0.987913,MA0099.2;0.902716,MA0079.2;1.22771,MA0102.2;1.88331,MA0258.1;0.519674,MA0259.1;0.575594,MA0442.1;0}}
|full_id=C3640_Eosinophils_Basophils_CD8_Dendritic_Natural_CD34_immature
|id=C3640
}}

Latest revision as of 12:30, 17 September 2013


Full id: C3640_Eosinophils_Basophils_CD8_Dendritic_Natural_CD34_immature



Phase1 CAGE Peaks

Hg19::chr17:43302954..43302970,+p@chr17:43302954..43302970
+
Hg19::chr17:74722536..74722639,-p1@JMJD6
Hg19::chr20:23331500..23331522,+p2@NXT1


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:0033749histone demethylase activity (H4-R3 specific)0.0024726245143059
GO:0033746histone demethylase activity (H3-R2 specific)0.0024726245143059
GO:0032452histone demethylase activity0.00618119735410036
GO:0032451demethylase activity0.00618119735410036
GO:0008536Ran GTPase binding0.0108779465636226
GO:0006611protein export from nucleus0.0115367065479968
GO:0006405RNA export from nucleus0.021184878106964
GO:0051168nuclear export0.0228100652115979
GO:0017016Ras GTPase binding0.0228100652115979
GO:0051213dioxygenase activity0.0228100652115979
GO:0016702oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen0.0228100652115979
GO:0016701oxidoreductase activity, acting on single donors with incorporation of molecular oxygen0.0228100652115979
GO:0031267small GTPase binding0.0228100652115979
GO:0005643nuclear pore0.0228100652115979
GO:0050658RNA transport0.0228100652115979
GO:0051236establishment of RNA localization0.0228100652115979
GO:0050657nucleic acid transport0.0228100652115979
GO:0006403RNA localization0.0228100652115979
GO:0007507heart development0.0228100652115979
GO:0051020GTPase binding0.0228100652115979
GO:0046930pore complex0.0228100652115979
GO:0015931nucleobase, nucleoside, nucleotide and nucleic acid transport0.0233421005353548
GO:0044453nuclear membrane part0.0238275617848449
GO:0031965nuclear membrane0.0292470614675695
GO:0006913nucleocytoplasmic transport0.0292470614675695
GO:0051169nuclear transport0.0292470614675695
GO:0001568blood vessel development0.0292470614675695
GO:0001944vasculature development0.0292470614675695
GO:0005635nuclear envelope0.032988036057757
GO:0006605protein targeting0.0358207019324699
GO:0019899enzyme binding0.0484371679013504



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
leukocyte3.08e-42136
hematopoietic stem cell2.36e-36168
angioblastic mesenchymal cell2.36e-36168
hematopoietic cell3.85e-36177
hematopoietic oligopotent progenitor cell1.69e-33161
hematopoietic multipotent progenitor cell1.69e-33161
hematopoietic lineage restricted progenitor cell3.40e-33120
nongranular leukocyte3.43e-31115
myeloid leukocyte2.39e-3072
granulocyte monocyte progenitor cell1.83e-2667
classical monocyte8.93e-2642
CD14-positive, CD16-negative classical monocyte8.93e-2642
defensive cell2.84e-2548
phagocyte2.84e-2548
myeloid cell1.07e-24108
common myeloid progenitor1.07e-24108
myeloid lineage restricted progenitor cell3.67e-2466
macrophage dendritic cell progenitor5.56e-2461
mesenchymal cell3.79e-23354
monopoietic cell1.31e-2259
monocyte1.31e-2259
monoblast1.31e-2259
promonocyte1.31e-2259
connective tissue cell1.48e-20361
motile cell7.49e-20386
multi fate stem cell1.66e-17427
somatic stem cell8.29e-17433
stem cell1.43e-16441
native cell1.60e-13722
somatic cell2.23e-11588
stuff accumulating cell1.42e-1087
animal cell1.77e-10679
eukaryotic cell1.77e-10679
lymphoid lineage restricted progenitor cell9.41e-0952
lymphocyte2.50e-0853
common lymphoid progenitor2.50e-0853
nucleate cell4.56e-0855
granulocyte4.45e-078
Uber Anatomy
Ontology termp-valuen
hematopoietic system1.77e-2598
blood island1.77e-2598
bone marrow7.44e-2476
bone element9.33e-2482
immune system4.04e-2293
hemolymphoid system4.80e-22108
connective tissue6.11e-20371
skeletal element2.93e-1890
lateral plate mesoderm6.23e-18203
skeletal system1.10e-13100
musculoskeletal system8.20e-08167


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
MA0006.10.639288
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
MA0048.10.341392
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.10.190716
MA0056.10
MA0057.10.886807
MA0058.10.716037
MA0059.11.70014
MA0060.10.492218
MA0061.10.456531
MA0063.10
MA0066.12.1667
MA0067.11.65513
MA0068.11.04561
MA0069.11.31207
MA0070.11.30033
MA0071.10.897953
MA0072.11.29561
MA0073.10.668628
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
MA0090.11.77664
MA0091.11.93651
MA0092.10.785956
MA0093.10.642957
MA0095.10
MA0098.10
MA0100.10.956299
MA0101.11.55947
MA0103.10.628063
MA0105.10.31555
MA0106.10.986396
MA0107.11.36919
MA0108.21.15387
MA0109.10
MA0111.10.767139
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
MA0144.11.31729
MA0145.10.273764
MA0146.10.707589
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.21.141
MA0035.20.894194
MA0039.22.74132
MA0138.21.04628
MA0002.20.476938
MA0137.21.60005
MA0104.21.2307
MA0047.20.973066
MA0112.20.731309
MA0065.20.760954
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.11.51687
MA0155.10.256269
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.12.02335
MA0161.10
MA0162.10.455568
MA0163.10.122425
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.21.22771
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
NFYA#4800212.28372046655370.008516011403724430.0324694697354547
NFYB#4801211.17319550235760.01025467135054530.0381215783149284
PPARGC1A#108911116.6837121212120.008545763211786680.0325650733052063
SIX5#147912211.3911435703060.009873820081429030.0370712835850152
SP2#6668217.43568699589640.004273568481769740.0203134543358615



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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