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Coexpression cluster:C3299: Difference between revisions

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{{Coexpression_clusters
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168748,0.0384949,0.0660995,0.0521984,0.0455518,0.268741,0.201602,0.350452,0.154941,0.120196,0.0986735,0.108462,0.0595618,0.21593,0.158479,0.220319,0.195218,0.124213,0.259632,0.0532009,0.180606,0.159884,0.257294,0.150733,0.217112,0.123917,0.184317,0.185335,0.0723291,0.258496,0.261744,0.203781,0.21382,0.207559,0.141867,0.193031,0.0339803,0.115972,0.0273485,0.246105,0.173026,0.200432,0.139785,0.0208458,0.240478,0.0129343,0.13108,0.256963,0.222798,0.172134,0.176789,0.0969345,0.202137,0.310405,0.280943,0.218161,0.0822373,0.202065,0.106739,0.0536053,0.0537737,0.15113,0.078016,0.0407233,0.0537355,0.319922,0.00371523,0.211332,0.187731,0.233626,0.00132285,0.0812887,0.0981146,0.064145,0.121913,0.0638699,0.104603,0.0663259,0.0762523,0.128736,0.109171,0.04411,0.066952,0.089609,0.0367455,0.13497,0.204393,0.00553696,0.0457063,0.347036,0.141729,0.263159,0.255956,0.200105,0.227491,0.00569858,0.253509,0.177664,0.28365,0.264413,0.131761,0.160658,0.206239,0.19924,0.28689,0.236464,0.325148,0.115817,0.218052,0.223831,0.11528,0.194982,0.190993,0.281727,0.0445413,0.249955,0.164638,0.224257,0.0935776,0.327622,0.225752,0.207791,0.0958756,0.0859274,0.316866,0.171683,0.158847,0.271275,0.071111,0.270604,0.101021,0.222548,0.175934,0.157274,0.0251447,0.252796,0.205954,0.361435|tfbs_overrepresentation_for_novel_motifs=0.699513,0.869629,0.690871,0.855819,0.641468,0.853988,0.937929,0.494933,0.491742,1.18351,0.820209,0.985163,0.436625,0.925331,0.639839,0.667627,1.17594,0.575162,0.452865,0.305559,0.69094,0.242883,0.845342,0.635379,0.743951,1.00973,1.05396,0.842925,0.645155,0.388328,0.795576,1.21459,2.27558,0.439574,0.599922,0.137917,0.596053,0.855276,1.39264,0.469078,0.598234,0.777097,0.259059,0.63803,0.901413,0.726632,0.939121,0.808003,0.247669,0.645308,1.02504,0.951993,0.336258,1.29475,1.45259,0.928548,0.650353,0.892517,0.388177,0.891404,1.25741,0.941709,0.492369,1.14672,0.961293,1.11026,1.54311,1.91674,1.2037,1.75271,3.00424,0.502203,0.333216,1.45054,0.430728,1.87308,0.396746,1.12884,1.20029,0.73687,0.459024,1.14559,0.960908,0.498519,1.39759,0.507157,2.26789,1.76229,1.053,2.0169,1.63834,1.36973,1.23218,0.543775,0.642354,0.560075,1.99742,1.27663,1.05794,0.360456,0.569121,1.22626,1.27082,1.1798,1.09802,0.815119,1.16312,2.12604,0.743661,0.622396,0.703975,1.26794,0.684398,0.830777,1.58942,0.594137,0.188952,1.86486,1.10778,1.35006,1.44203,1.0504,0.850918,0.973172,1.70203,1.12965,0.930979,1.2374,1.48578,1.37952,1.37044,0.798812,1.50051,0.969553,1.65144,3.57034,0.788803,0.843556,1.60823,2.47382,2.06967,1.57016,0.932872,1.27296,1.09989,0.883164,1.08214,2.31409,0.773313,0.539692,0.853445,0.698641,1.37083,1.21015,0.941179,1.78371,1.03563,0.624795,0.744018,1.69223,1.56892,1.35169,1.19946,0.714443,1.11698,0.960047,0.524529,0.936473,0.56135|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;0.758317,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;0.341392,MA0050.1;0.81185,MA0051.1;0.936307,MA0052.1;1.24796,MA0055.1;0.190716,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;1.79391,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;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;0.846801,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;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;2.4174,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;0.107247,MA0147.1;0.565108,MA0148.1;0.854239,MA0149.1;0.884158,MA0062.2;0.449458,MA0035.2;0.894194,MA0039.2;2.15877,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;0.760954,MA0150.1;0.744617,MA0151.1;0,MA0152.1;0.902317,MA0153.1;1.43021,MA0154.1;0.312019,MA0155.1;2.02721,MA0156.1;0.669101,MA0157.1;1.09377,MA0158.1;0,MA0159.1;2.37721,MA0160.1;0.871361,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;2.08754,MA0079.2;3.61229,MA0102.2;1.88331,MA0258.1;0.519674,MA0259.1;0.575594,MA0442.1;0}}
|full_id=C3299_serous_signet_skeletal_optic_colon_breast_Hepatocyte
|id=C3299
}}

Latest revision as of 12:23, 17 September 2013


Full id: C3299_serous_signet_skeletal_optic_colon_breast_Hepatocyte



Phase1 CAGE Peaks

Hg19::chr12:56473883..56473903,+p2@ERBB3
Hg19::chr12:56473910..56473921,+p4@ERBB3
Hg19::chr12:56473939..56473994,+p1@ERBB3


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
epithelial cell9.81e-18253
endodermal cell3.10e-1058
Uber Anatomy
Ontology termp-valuen
adult organism2.55e-29114
organ system subdivision9.62e-22223
endoderm-derived structure3.70e-16160
endoderm3.70e-16160
presumptive endoderm3.70e-16160
neural tube1.80e-1556
neural rod1.80e-1556
future spinal cord1.80e-1556
neural keel1.80e-1556
regional part of nervous system5.40e-1453
regional part of brain5.40e-1453
organ1.50e-13503
digestive system2.41e-13145
digestive tract2.41e-13145
primitive gut2.41e-13145
subdivision of digestive tract2.59e-13118
multi-tissue structure3.50e-13342
organ part6.33e-13218
regional part of forebrain1.02e-1141
forebrain1.02e-1141
anterior neural tube1.02e-1141
future forebrain1.02e-1141
central nervous system2.83e-1181
telencephalon6.14e-1134
ecto-epithelium6.92e-11104
brain grey matter7.36e-1134
gray matter7.36e-1134
brain1.05e-1068
future brain1.05e-1068
anatomical cluster5.05e-10373
regional part of telencephalon8.20e-1032
neural plate9.23e-1082
presumptive neural plate9.23e-1082
cerebral hemisphere1.15e-0932
nervous system1.65e-0989
ectoderm-derived structure3.42e-09171
ectoderm3.42e-09171
presumptive ectoderm3.42e-09171
immaterial anatomical entity6.28e-09117
regional part of cerebral cortex1.03e-0822
endo-epithelium1.07e-0882
neurectoderm1.73e-0886
foregut2.03e-0887
anatomical conduit4.71e-08240
neocortex6.16e-0820
pre-chordal neural plate1.89e-0761
epithelium2.22e-07306
trunk region element3.56e-07101
multi-cellular organism5.34e-07656
cell layer5.73e-07309
cerebral cortex8.13e-0725
pallium8.13e-0725
Disease
Ontology termp-valuen
carcinoma2.11e-16106
cell type cancer2.23e-12143
adenocarcinoma2.36e-0725


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
MA0014.10.758317
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
MA0048.10.341392
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.10.190716
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
MA0073.11.79391
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
MA0092.10.785956
MA0093.10.642957
MA0095.10
MA0098.10
MA0100.10.956299
MA0101.10.646932
MA0103.10.628063
MA0105.10.846801
MA0106.10.986396
MA0107.10.556367
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
MA0131.12.4174
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
MA0146.10.107247
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.22.15877
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.20.491226
MA0047.20.973066
MA0112.20.731309
MA0065.20.760954
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.10.312019
MA0155.12.02721
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.12.37721
MA0160.10.871361
MA0161.10
MA0162.10.455568
MA0163.10.122425
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.22.08754
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
CCNT2#90536.336201576962630.003930750035764890.0189460773022544
CEBPB#105137.971147625824820.001974187055288560.0115018476998372
CHD2#1106310.34402283411690.0009033701102746880.00659032348050979
CTCF#1066435.360256373075030.0064925092527670.027868610983919
E2F6#187635.017155731697390.00791769806886330.0320945650539109
EGR1#195834.988179094810140.008056488137383440.0319478894551463
FOS#235338.99795530889440.001372499272417130.00895442600649504
FOSL1#8061339.7135797163731.59554825631833e-050.000370470129705714
FOSL2#2355316.93020060456170.0002060162053171620.00242517205445436
FOXA1#3169311.08141974938550.000734755275698670.00579979640531277
HDAC2#3066313.41562023662630.0004140761399857210.0039023369413435
HMGN3#932438.178547723350590.001827766942164210.0108441829047713
JUN#3725312.51282919233630.0005103313992726250.00443378263111502
JUNB#3726330.61063265982113.4847716247536e-050.000679764780944418
JUND#372736.994663941871030.002921845042734990.0156321179457097
MYC#460935.22228187160940.007020843755740150.0293534788232885
SIN3A#2594235.408884726815140.006318961977991520.0275747323787012
SMARCB1#6598318.25271578115740.000164397760679890.00202686078711451
SMARCC1#6599343.66335931963151.20046018043203e-050.000301164690809851
SP1#666735.69838137814090.005403962701712170.0245705032914287
TAF7#6879311.43306940492390.0006690181981945830.00541304552225318
ZBTB7A#5134137.35190930787590.002516255860282270.0139762402697452
ZNF263#1012738.221841637010680.001799043925565870.0109048374081355



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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