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Coexpression cluster:C4573: Difference between revisions

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{{Coexpression_clusters
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86691,0.347036,0.141729,0.263159,0.255956,0.200105,0.227491,0.29837,0.00335066,0.177664,0.28365,0.264413,0.131761,0.160658,0.206239,0.19924,0.28689,0.236464,0.325148,0.115817,0.00206474,0.223831,0.11528,0.00144649,0.190993,0.281727,0.283218,0.249955,0.164638,0.224257,0.0935776,0.327622,0.225752,0.207791,0.0958756,0.0859274,0.316866,0.171683,0.158847,0.271275,0.071111,0.270604,0.101021,0.222548,0.175934,0.157274,0.215705,0.252796,0.205954,0.361435|tfbs_overrepresentation_for_novel_motifs=1.66899,0.442617,1.65103,0.855819,0.641468,0.853988,0.937929,0.494933,0.491742,0.221898,0.820209,0.985163,0.436625,0.925331,0.639839,0.667627,1.17594,0.575162,2.00385,0.305559,0.69094,1.26332,0.845342,0.635379,0.743951,1.00973,0.409304,0.842925,0.645155,0.388328,0.795576,1.21459,1.3235,1.11965,0.599922,0.137917,1.45286,0.855276,0.567465,2.05816,0.598234,3.05144,0.259059,0.63803,0.151453,0.726632,0.939121,0.808003,0.247669,0.645308,1.02504,0.951993,0.336258,1.29475,1.45259,0.928548,0.650353,0.892517,0.388177,0.891404,1.25741,0.941709,0.492369,1.14672,0.961293,7.5726,1.54311,1.91674,1.2037,1.75271,0.762094,1.25415,0.333216,1.45054,0.430728,0.414196,0.396746,1.12884,1.20029,0.73687,0.459024,1.14559,0.960908,1.24629,1.39759,1.55552,0.303648,0.381882,1.053,2.0169,1.63834,1.36973,1.23218,0.543775,0.642354,0.560075,0.450952,1.27663,1.05794,0.360456,0.569121,1.22626,1.27082,1.1798,1.09802,0.815119,1.16312,0.921547,0.743661,3.73269,0.703975,1.26794,0.684398,0.830777,1.58942,0.594137,0.553386,1.86486,1.10778,0.547323,1.44203,1.0504,0.850918,0.973172,1.70203,1.12965,0.930979,1.2374,1.48578,0.561252,1.37044,0.798812,1.50051,0.969553,1.65144,0.974093,0.788803,0.843556,1.60823,2.47382,2.06967,1.57016,0.932872,1.27296,1.09989,0.883164,1.08214,2.31409,0.773313,2.29164,3.23473,0.698641,1.37083,0.481626,0.941179,1.78371,1.03563,0.624795,0.744018,0.710709,1.56892,1.35169,1.19946,0.714443,1.11698,0.960047,2.24188,0.936473,21.7802|tfbs_overrepresentation_jaspar=MA0003.1;8.53684,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;0.557638,MA0056.1;0,MA0057.1;0.333427,MA0058.1;0.716037,MA0059.1;0.714521,MA0060.1;0.492218,MA0061.1;2.01615,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;1.70054,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;1.55947,MA0103.1;0.628063,MA0105.1;2.3269,MA0106.1;0.986396,MA0107.1;2.34614,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;3.02823,MA0119.1;1.66081,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;5.09957,MA0140.1;0.894983,MA0141.1;0.712476,MA0142.1;1.12317,MA0143.1;1.00455,MA0144.1;0.531867,MA0145.1;12.9155,MA0146.1;7.1063,MA0147.1;0.565108,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;0.491226,MA0047.2;0.973066,MA0112.2;2.07067,MA0065.2;0.760954,MA0150.1;0.744617,MA0151.1;0,MA0152.1;0.902317,MA0153.1;1.43021,MA0154.1;0.312019,MA0155.1;3.71118,MA0156.1;0.669101,MA0157.1;1.09377,MA0158.1;0,MA0159.1;0.565904,MA0160.1;0.871361,MA0161.1;0,MA0162.1;0.8915,MA0163.1;3.19905,MA0164.1;1.01792,MA0080.2;2.62633,MA0018.2;0.987913,MA0099.2;0.902716,MA0079.2;0.69213,MA0102.2;1.88331,MA0258.1;0.519674,MA0259.1;0.575594,MA0442.1;0}}
|full_id=C4573_Melanocyte_Monocytederived_Osteoblast_Alveolar_Smooth_mesothelioma_Hepatic
|id=C4573
}}

Latest revision as of 14:15, 17 September 2013


Full id: C4573_Melanocyte_Monocytederived_Osteoblast_Alveolar_Smooth_mesothelioma_Hepatic



Phase1 CAGE Peaks

Hg19::chr6:146864862..146864881,+p3@RAB32
Hg19::chr6:146864935..146864949,+p2@RAB32
Hg19::chr6:146864960..146864999,+p1@RAB32


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
somatic cell2.34e-37588
animal cell1.61e-30679
eukaryotic cell1.61e-30679
mesodermal cell1.90e-23121
granulocyte monocyte progenitor cell2.00e-2167
myeloid leukocyte3.72e-2172
embryonic cell1.58e-20250
native cell2.36e-20722
defensive cell6.15e-2048
phagocyte6.15e-2048
macrophage dendritic cell progenitor1.23e-1961
monopoietic cell2.31e-1959
monocyte2.31e-1959
monoblast2.31e-1959
promonocyte2.31e-1959
myeloid lineage restricted progenitor cell4.52e-1966
classical monocyte5.37e-1842
CD14-positive, CD16-negative classical monocyte5.37e-1842
stuff accumulating cell1.37e-1787
contractile cell1.72e-1459
muscle cell7.50e-1455
smooth muscle cell1.02e-1343
smooth muscle myoblast1.02e-1343
muscle precursor cell2.07e-1358
myoblast2.07e-1358
multi-potent skeletal muscle stem cell2.07e-1358
multi fate stem cell9.87e-13427
somatic stem cell2.10e-12433
stem cell5.16e-12441
non-terminally differentiated cell9.44e-11106
myeloid cell1.70e-10108
common myeloid progenitor1.70e-10108
vascular associated smooth muscle cell2.72e-1032
lining cell3.18e-1058
barrier cell3.18e-1058
electrically responsive cell5.77e-1061
electrically active cell5.77e-1061
meso-epithelial cell3.44e-0945
endothelial cell3.56e-0936
columnar/cuboidal epithelial cell1.07e-0727
epithelial cell4.57e-07253
Uber Anatomy
Ontology termp-valuen
lateral plate mesoderm1.82e-32203
mesoderm5.59e-31315
mesoderm-derived structure5.59e-31315
presumptive mesoderm5.59e-31315
musculoskeletal system2.52e-30167
bone marrow3.45e-2176
skeletal element1.27e-1990
bone element1.98e-1982
skeletal system1.97e-18100
immune system1.46e-1793
epithelial tube1.02e-15117
hemolymphoid system3.79e-15108
epithelial vesicle5.28e-1578
hematopoietic system1.62e-1498
blood island1.62e-1498
vasculature6.13e-1478
vascular system6.13e-1478
unilaminar epithelium6.28e-14148
anatomical system1.13e-13624
cardiovascular system1.53e-13109
anatomical group2.46e-13625
splanchnic layer of lateral plate mesoderm2.84e-1383
somite7.26e-1371
presomitic mesoderm7.26e-1371
presumptive segmental plate7.26e-1371
dermomyotome7.26e-1371
trunk paraxial mesoderm7.26e-1371
developing anatomical structure8.74e-13581
dense mesenchyme tissue1.21e-1273
trunk mesenchyme1.67e-12122
multilaminar epithelium1.83e-1283
circulatory system1.98e-12112
paraxial mesoderm2.35e-1272
presumptive paraxial mesoderm2.35e-1272
vessel8.34e-1268
multi-cellular organism9.43e-12656
embryonic structure9.88e-12564
embryo1.24e-11592
skeletal muscle tissue1.83e-1162
striated muscle tissue1.83e-1162
myotome1.83e-1162
artery2.00e-1142
arterial blood vessel2.00e-1142
arterial system2.00e-1142
mesenchyme2.22e-11160
entire embryonic mesenchyme2.22e-11160
epithelial tube open at both ends2.44e-1159
blood vessel2.44e-1159
blood vasculature2.44e-1159
vascular cord2.44e-1159
germ layer4.98e-11560
germ layer / neural crest4.98e-11560
embryonic tissue4.98e-11560
presumptive structure4.98e-11560
germ layer / neural crest derived structure4.98e-11560
epiblast (generic)4.98e-11560
muscle tissue6.90e-1164
musculature6.90e-1164
musculature of body6.90e-1164


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)
MA0003.18.53684
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
MA0055.10.557638
MA0056.10
MA0057.10.333427
MA0058.10.716037
MA0059.10.714521
MA0060.10.492218
MA0061.12.01615
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
MA0081.11.70054
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
MA0101.11.55947
MA0103.10.628063
MA0105.12.3269
MA0106.10.986396
MA0107.12.34614
MA0108.21.15387
MA0109.10
MA0111.10.767139
MA0113.11.00436
MA0114.10.549955
MA0115.11.57693
MA0116.10.560723
MA0117.13.02823
MA0119.11.66081
MA0122.11.39371
MA0124.11.53432
MA0125.11.44766
MA0130.10
MA0131.11.06461
MA0132.10
MA0133.10
MA0135.11.35921
MA0136.10.948776
MA0139.15.09957
MA0140.10.894983
MA0141.10.712476
MA0142.11.12317
MA0143.11.00455
MA0144.10.531867
MA0145.112.9155
MA0146.17.1063
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.21.15986
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.20.491226
MA0047.20.973066
MA0112.22.07067
MA0065.20.760954
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.10.312019
MA0155.13.71118
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.10.8915
MA0163.13.19905
MA0164.11.01792
MA0080.22.62633
MA0018.20.987913
MA0099.20.902716
MA0079.20.69213
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
CCNT2#90536.336201576962630.003930750035764890.0190967857368586
CTCF#1066435.360256373075030.0064925092527670.0281077422421544
CTCFL#140690319.74647435897440.0001298372005551160.00172256953617579
E2F1#186934.907389214879320.008460985347239390.0327377315011979
E2F6#187635.017155731697390.00791769806886330.0324026829394206
ELF1#199734.258097958807540.01295179875054610.0464596568678785
GABPB1#255337.067683836182170.002832212825417420.0154727977859377
HMGN3#932438.178547723350590.001827766942164210.0109105024961527
HNF4A#3172323.13229036295378.07584663437677e-050.00123345034607733
RAD21#5885310.35503389545630.0009004912073565420.00667990632893741
SMC3#9126315.04493284493280.0002935825420371870.00310590225970641
SPI1#668838.204323508522730.001810593189410520.0109373903701108
TAF7#6879311.43306940492390.0006690181981945830.00545275414400219
USF1#739136.361499277207960.00388404057290560.0191035750868272
ZBTB7A#5134137.35190930787590.002516255860282270.0140795738436657



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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