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{{Coexpression_clusters
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1057,0.15696,0.129351,0.0105865,0.0786166,0.276997,0.205513,0.282389,0.251421,0.0139099,0.330223,0.387837,0.233244,0.207281,0.327401,0.195748,0.27845,0.161712,0.237871,0.239139,0.095257,0.000767461,0.00817635,0.262022,0.274403,0.266687,0.184534,0.248707,0.00699456,0.15156,0.00505104,0.313858,0.223773,0.25788,0.0176484,1.40447e-05,0.30702,0.00164332,0.170837,0.00771419,0.00492748,6.85234e-06,0.228479,0.000378293,0.259989,0.0140513,0.355805,0.279739,0.108118,0.259901,0.139723,0.0708274,0.0710478,0.196248,0.102645,0.0539258,0.0709978,0.401939,0.332746,0.271338,0.242121,0.298673,0.244395,0.106889,0.128632,0.0845989,0.159153,0.0842401,0.000477314,0.0874421,0.100355,0.167854,0.142846,0.0583767,0.088258,0.117657,0.0486914,0.00104239,0.262778,0.373453,0.362662,0.111581,0.184359,0.334474,0.00761927,0.257476,0.291176,0.376537,0.322827,0.229571,0.359036,0.335984,0.171704,0.0233701,0.0387226,0.000253547,0.362898,0.302133,0.40806,0.151361,0.279606,0.286696,0.150674,0.251128,0.00304766,0.35674,0.35852,0.318525,0.00192326,0.287217,0.122782,0.00214888,0.289049,0.266974,0.125746,0.00662717,0.398354,0.222091,0.205977,0.34423,0.0936726,0.00908363,0.132374,0.285122,0.22741,0.203996,0.276721,0.321965,0.264707,0.121257|tfbs_overrepresentation_for_novel_motifs=0.590005,1.03954,0.581696,0.741427,0.534346,0.739643,0.821651,0.395818,0.392841,0.151681,0.706765,0.867962,0.341754,0.809319,0.532789,0.559384,1.05593,0.471262,0.356737,0.635753,0.581762,0.975621,0.731221,0.528529,0.632849,0.892087,0.849366,0.728867,0.537869,0.806311,0.682839,1.09415,1.93746,0.344471,0.49475,0.0842336,0.491074,0.740899,0.463978,0.371755,0.493145,0.66492,1.03152,0.53106,0.0946706,0.61613,0.822818,0.694903,0.515703,0.538016,0.90714,1.94963,0.25073,2.63818,1.33024,1.90242,1.34056,0.777235,0.297448,0.776148,1.13655,0.825354,0.393426,1.02706,0.844545,0.991076,1.42026,1.79268,1.08337,1.62905,0.650393,0.402607,0.248021,1.32819,0.336329,0.321165,0.305238,1.00941,1.08,0.62601,0.362435,2.33882,0.844168,1.03184,1.27559,2.34631,1.18341,0.291738,0.934646,1.89266,1.51507,1.24792,1.11156,0.441618,0.535192,0.456994,0.354969,1.15558,0.939507,0.272395,0.465545,1.1057,1.14983,1.05974,0.979006,0.701817,1.04326,0.805616,1.52945,0.516141,0.594299,1.14697,0.575476,0.717043,1.46636,0.489254,0.393155,0.681522,0.988625,0.444962,1.31973,0.932085,0.736652,0.856196,1.57854,1.0102,0.814847,1.11673,1.36323,0.458105,1.24863,0.68598,1.37788,0.852645,1.52813,0.283547,0.676268,0.729481,1.48509,2.34913,1.94535,1.44718,0.8167,1.15194,0.980848,0.768101,0.963351,2.1895,0.661255,3.95711,0.234974,0.175846,1.24902,0.383416,0.824835,1.65997,0.917558,0.518428,0.632914,0.600782,1.44595,1.23002,1.07918,0.604379,0.997702,0.843324,0.423521,0.820225,3.03252|tfbs_overrepresentation_jaspar=MA0003.1;0.720743,MA0004.1;0.71247,MA0006.1;3.33615,MA0007.1;0.6918,MA0009.1;1.20602,MA0014.1;0.244769,MA0017.1;0.577281,MA0019.1;0.873355,MA0024.1;1.09684,MA0025.1;1.34373,MA0027.1;2.83281,MA0028.1;0.550763,MA0029.1;1.11704,MA0030.1;1.10506,MA0031.1;1.03735,MA0038.1;0.824639,MA0040.1;1.12314,MA0041.1;0.732902,MA0042.1;0.697662,MA0043.1;1.20635,MA0046.1;1.19471,MA0048.1;0.25531,MA0050.1;0.69864,MA0051.1;0.820063,MA0052.1;1.12718,MA0055.1;0.125954,MA0056.1;0,MA0057.1;0.248209,MA0058.1;0.605914,MA0059.1;0.604454,MA0060.1;0.393285,MA0061.1;0.360128,MA0063.1;0,MA0066.1;0.825101,MA0067.1;1.53181,MA0068.1;0.313194,MA0069.1;1.19071,MA0070.1;1.17908,MA0071.1;0.782546,MA0072.1;1.1744,MA0073.1;0.0343867,MA0074.1;0.819248,MA0076.1;0.623864,MA0077.1;1.16637,MA0078.1;0.926725,MA0081.1;0.604638,MA0083.1;1.21381,MA0084.1;1.72172,MA0087.1;1.17185,MA0088.1;0.182167,MA0089.1;0,MA0090.1;0.640115,MA0091.1;0.715356,MA0092.1;0.673508,MA0093.1;0.535768,MA0095.1;0,MA0098.1;0,MA0100.1;0.83965,MA0101.1;0.539569,MA0103.1;0.521546,MA0105.1;0.656404,MA0106.1;0.869173,MA0107.1;0.453492,MA0108.2;1.03412,MA0109.1;0,MA0111.1;0.655276,MA0113.1;0.886811,MA0114.1;0.447443,MA0115.1;1.45393,MA0116.1;0.457606,MA0117.1;1.24497,MA0119.1;0.586221,MA0122.1;1.27173,MA0124.1;1.41151,MA0125.1;1.32534,MA0130.1;0,MA0131.1;0.94608,MA0132.1;0,MA0133.1;0,MA0135.1;1.23748,MA0136.1;0.832277,MA0139.1;1.63368,MA0140.1;0.779643,MA0141.1;0.602484,MA0142.1;1.00381,MA0143.1;0.887001,MA0144.1;0.430413,MA0145.1;0.195821,MA0146.1;0.221129,MA0147.1;0.46175,MA0148.1;0.739888,MA0149.1;0.769072,MA0062.2;0.353589,MA0035.2;0.778873,MA0039.2;0.777367,MA0138.2;3.52208,MA0002.2;0.379056,MA0137.2;0.558189,MA0104.2;0.392359,MA0047.2;0.856092,MA0112.2;0.187982,MA0065.2;0.199162,MA0150.1;0.633493,MA0151.1;0,MA0152.1;0.78681,MA0153.1;1.30799,MA0154.1;0.229241,MA0155.1;1.61785,MA0156.1;0.560797,MA0157.1;0.97481,MA0158.1;0,MA0159.1;0.462502,MA0160.1;0.756582,MA0161.1;0,MA0162.1;0.0928415,MA0163.1;0.0725493,MA0164.1;0.90014,MA0080.2;0.535868,MA0018.2;0.870662,MA0099.2;0.7872,MA0079.2;0.869502,MA0102.2;1.75932,MA0258.1;0.418966,MA0259.1;0.471671,MA0442.1;0}}
|full_id=C2668_kidney_choriocarcinoma_thyroid_mesothelioma_optic_substantia_colon
|id=C2668
|ontology_enrichment_celltype=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0001049!2.59e-48!57;UBERON:0005068!2.59e-48!57;UBERON:0006241!2.59e-48!57;UBERON:0007135!2.59e-48!57;UBERON:0003075!8.34e-46!86;UBERON:0007284!8.34e-46!86;UBERON:0002346!4.36e-44!90;UBERON:0002616!1.54e-41!59;UBERON:0007023!2.54e-41!115;UBERON:0005743!9.08e-41!86;UBERON:0001017!9.54e-39!82;UBERON:0000955!3.66e-37!69;UBERON:0006238!3.66e-37!69;UBERON:0003080!8.08e-37!42;UBERON:0000073!1.33e-36!94;UBERON:0001016!1.33e-36!94;UBERON:0002780!1.07e-35!41;UBERON:0001890!1.07e-35!41;UBERON:0006240!1.07e-35!41;UBERON:0003056!2.08e-35!61;UBERON:0001893!6.15e-33!34;UBERON:0002020!6.51e-33!34;UBERON:0003528!6.51e-33!34;UBERON:0002791!8.36e-32!33;UBERON:0001869!2.54e-30!32;UBERON:0000153!1.29e-24!129;UBERON:0007811!1.29e-24!129;UBERON:0000956!7.73e-23!25;UBERON:0000203!7.73e-23!25;UBERON:0000033!8.31e-23!123;UBERON:0002619!1.78e-20!22;UBERON:0004121!2.74e-19!169;UBERON:0000924!5.50e-19!173;UBERON:0006601!5.50e-19!173;UBERON:0001950!1.87e-18!20;UBERON:0000064!2.45e-14!219;UBERON:0004732!2.14e-12!13;UBERON:0003076!2.80e-12!15;UBERON:0003057!2.80e-12!15;UBERON:0000025!4.25e-12!194;UBERON:0002308!1.36e-11!9;UBERON:0000125!1.36e-11!9;UBERON:0002298!2.96e-11!8;UBERON:0002420!3.65e-11!9;UBERON:0007245!3.65e-11!9;UBERON:0010009!3.65e-11!9;UBERON:0010011!3.65e-11!9;UBERON:0000454!3.65e-11!9;UBERON:0004733!3.81e-11!12;UBERON:0002028!3.81e-11!12;UBERON:0007277!3.81e-11!12;UBERON:0000477!9.30e-11!286;UBERON:0000483!5.90e-10!309;UBERON:0000062!1.20e-09!511;UBERON:0000119!1.24e-09!312;UBERON:0000481!1.90e-09!347;UBERON:0009663!3.13e-09!7;UBERON:0000063!1.92e-08!97;UBERON:0001737!2.19e-08!9;UBERON:0000200!6.29e-08!6;UBERON:0002680!1.11e-07!9;UBERON:0001895!1.11e-07!9;UBERON:0010092!1.11e-07!9;UBERON:0001871!2.15e-07!7;UBERON:0000922!2.50e-07!612;UBERON:0004111!3.69e-07!241;UBERON:0001872!8.56e-07!5
}}

Latest revision as of 12:10, 17 September 2013


Full id: C2668_kidney_choriocarcinoma_thyroid_mesothelioma_optic_substantia_colon



Phase1 CAGE Peaks

Hg19::chr2:169984040..169984044,-p@chr2:169984040..169984044
-
Hg19::chr2:170219007..170219018,-p2@LRP2
Hg19::chr2:170219037..170219050,-p1@LRP2
Hg19::chr2:170219079..170219084,-p3@LRP2


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
embryonic stem cell4.55e-085
Uber Anatomy
Ontology termp-valuen
adult organism4.97e-43114
neural tube5.30e-4256
neural rod5.30e-4256
future spinal cord5.30e-4256
neural keel5.30e-4256
regional part of nervous system5.09e-4053
regional part of brain5.09e-4053
neural plate1.62e-3882
presumptive neural plate1.62e-3882
neurectoderm5.05e-3686
pre-chordal neural plate4.98e-3361
regional part of forebrain1.53e-3241
forebrain1.53e-3241
anterior neural tube1.53e-3241
future forebrain1.53e-3241
telencephalon4.03e-3234
brain grey matter5.40e-3234
gray matter5.40e-3234
brain1.07e-3168
future brain1.07e-3168
central nervous system6.33e-3181
regional part of telencephalon5.79e-2932
cerebral hemisphere9.44e-2932
ecto-epithelium9.49e-29104
nervous system3.51e-2889
structure with developmental contribution from neural crest2.98e-24132
cerebral cortex3.38e-1925
pallium3.38e-1925
regional part of cerebral cortex3.74e-1822
neocortex7.71e-1820
organ system subdivision2.22e-17223
ectoderm-derived structure1.74e-15171
ectoderm1.74e-15171
presumptive ectoderm1.74e-15171
neural nucleus2.83e-159
nucleus of brain2.83e-159
basal ganglion1.29e-149
nuclear complex of neuraxis1.29e-149
aggregate regional part of brain1.29e-149
collection of basal ganglia1.29e-149
cerebral subcortex1.29e-149
organ part2.23e-12218
anatomical cluster2.58e-12373
telencephalic nucleus4.22e-127
multi-tissue structure6.85e-12342
brainstem1.59e-116
posterior neural tube1.95e-1015
chordal neural plate1.95e-1015
segmental subdivision of nervous system4.30e-1013
tube1.69e-09192
organ6.20e-09503
segmental subdivision of hindbrain1.31e-0812
hindbrain1.31e-0812
presumptive hindbrain1.31e-0812
temporal lobe3.13e-086
epithelium7.24e-08306
cell layer1.22e-07309
gyrus1.85e-076
embryo2.65e-07592
corpus striatum6.72e-074
striatum6.72e-074
ventral part of telencephalon6.72e-074
future corpus striatum6.72e-074


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)
MA0003.10.720743
MA0004.10.71247
MA0006.13.33615
MA0007.10.6918
MA0009.11.20602
MA0014.10.244769
MA0017.10.577281
MA0019.10.873355
MA0024.11.09684
MA0025.11.34373
MA0027.12.83281
MA0028.10.550763
MA0029.11.11704
MA0030.11.10506
MA0031.11.03735
MA0038.10.824639
MA0040.11.12314
MA0041.10.732902
MA0042.10.697662
MA0043.11.20635
MA0046.11.19471
MA0048.10.25531
MA0050.10.69864
MA0051.10.820063
MA0052.11.12718
MA0055.10.125954
MA0056.10
MA0057.10.248209
MA0058.10.605914
MA0059.10.604454
MA0060.10.393285
MA0061.10.360128
MA0063.10
MA0066.10.825101
MA0067.11.53181
MA0068.10.313194
MA0069.11.19071
MA0070.11.17908
MA0071.10.782546
MA0072.11.1744
MA0073.10.0343867
MA0074.10.819248
MA0076.10.623864
MA0077.11.16637
MA0078.10.926725
MA0081.10.604638
MA0083.11.21381
MA0084.11.72172
MA0087.11.17185
MA0088.10.182167
MA0089.10
MA0090.10.640115
MA0091.10.715356
MA0092.10.673508
MA0093.10.535768
MA0095.10
MA0098.10
MA0100.10.83965
MA0101.10.539569
MA0103.10.521546
MA0105.10.656404
MA0106.10.869173
MA0107.10.453492
MA0108.21.03412
MA0109.10
MA0111.10.655276
MA0113.10.886811
MA0114.10.447443
MA0115.11.45393
MA0116.10.457606
MA0117.11.24497
MA0119.10.586221
MA0122.11.27173
MA0124.11.41151
MA0125.11.32534
MA0130.10
MA0131.10.94608
MA0132.10
MA0133.10
MA0135.11.23748
MA0136.10.832277
MA0139.11.63368
MA0140.10.779643
MA0141.10.602484
MA0142.11.00381
MA0143.10.887001
MA0144.10.430413
MA0145.10.195821
MA0146.10.221129
MA0147.10.46175
MA0148.10.739888
MA0149.10.769072
MA0062.20.353589
MA0035.20.778873
MA0039.20.777367
MA0138.23.52208
MA0002.20.379056
MA0137.20.558189
MA0104.20.392359
MA0047.20.856092
MA0112.20.187982
MA0065.20.199162
MA0150.10.633493
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.10.229241
MA0155.11.61785
MA0156.10.560797
MA0157.10.97481
MA0158.10
MA0159.10.462502
MA0160.10.756582
MA0161.10
MA0162.10.0928415
MA0163.10.0725493
MA0164.10.90014
MA0080.20.535868
MA0018.20.870662
MA0099.20.7872
MA0079.20.869502
MA0102.21.75932
MA0258.10.418966
MA0259.10.471671
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
HNF4A#3172317.34921777221530.0003125641557482750.0032155129887898
HNF4G#3174321.56506689483510.0001638032421292610.00203684329143206
SUZ12#23512337.58683568329723.12785741999833e-050.000631857448911422



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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