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{{Coexpression_clusters
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0.108118,0.259901,0.139723,0.0708274,0.0710478,0.196248,0.102645,0.0539258,0.0709978,0.401939,0.332746,0.271338,0.242121,0.298673,0.244395,0.106889,0.128632,0.0845989,0.159153,0.0842401,0.13698,0.0874421,0.100355,0.167854,0.142846,0.0583767,0.088258,0.117657,0.0486914,0.175784,0.262778,0.0805224,0.362662,0.433518,0.184359,0.334474,0.325785,0.257476,0.291176,0.376537,0.322827,0.229571,0.359036,0.335984,0.171704,0.0233701,0.265058,0.256405,0.362898,0.302133,0.40806,0.151361,0.279606,0.286696,0.150674,0.251128,0.246177,0.35674,0.35852,0.318525,0.213257,0.287217,0.122782,0.410951,0.289049,0.266974,0.125746,0.112897,0.398354,0.222091,0.205977,0.34423,0.0936726,0.343425,0.132374,0.285122,0.22741,0.203996,0.276721,0.321965,0.264707,0.450113|tfbs_overrepresentation_for_novel_motifs=0.590005,0.298605,0.581696,0.741427,0.534346,0.739643,0.821651,0.395818,0.392841,2.07992,1.68405,0.867962,0.341754,0.809319,0.532789,0.559384,1.05593,0.471262,0.356737,0.223552,0.581762,0.505745,0.731221,0.528529,0.632849,0.892087,0.316693,0.728867,0.537869,0.806311,0.682839,1.09415,1.93746,0.344471,0.49475,0.0842336,3.15145,1.75478,0.463978,0.371755,0.493145,0.66492,0.183156,0.53106,2.82841,0.61613,1.92371,0.694903,0.173425,0.538016,0.90714,1.94963,0.25073,1.17354,1.33024,0.812467,0.54284,0.777235,0.806003,0.776148,1.13655,0.825354,0.393426,1.02706,1.96835,0.991076,1.42026,1.79268,1.08337,1.62905,0.650393,0.402607,4.57517,1.32819,5.3994,0.859396,0.305238,1.00941,1.08,0.62601,0.362435,2.33882,0.844168,0.399165,1.27559,8.09613,0.221873,0.291738,0.934646,1.89266,1.51507,1.24792,1.11156,0.441618,2.27689,0.456994,0.354969,1.15558,0.939507,0.272395,0.465545,1.1057,1.14983,1.05974,0.979006,0.701817,1.04326,0.805616,0.632569,0.516141,0.594299,1.14697,1.40954,0.717043,1.46636,0.489254,2.51097,0.681522,0.988625,0.444962,1.31973,0.932085,0.736652,0.856196,1.57854,1.0102,0.814847,1.11673,1.36323,1.15964,1.24863,2.76338,1.37788,0.852645,1.52813,0.283547,0.676268,0.729481,1.48509,2.34913,1.94535,1.44718,0.8167,1.15194,0.980848,0.768101,0.963351,2.1895,0.661255,3.95711,0.234974,4.697,1.24902,0.383416,0.824835,1.65997,0.917558,0.518428,0.632914,0.600782,1.44595,1.23002,1.07918,0.604379,0.997702,0.843324,1.90479,0.820225,6.53028|tfbs_overrepresentation_jaspar=MA0003.1;3.49532,MA0004.1;0.71247,MA0006.1;1.31813,MA0007.1;0.6918,MA0009.1;1.20602,MA0014.1;9.60141,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;3.20044,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;0.791759,MA0056.1;0,MA0057.1;0.248209,MA0058.1;0.605914,MA0059.1;0.604454,MA0060.1;2.70115,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;0.866596,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;0.232357,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;1.13665,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;0.344952,MA0140.1;0.779643,MA0141.1;0.602484,MA0142.1;1.00381,MA0143.1;0.887001,MA0144.1;0.430413,MA0145.1;1.08195,MA0146.1;1.25938,MA0147.1;0.46175,MA0148.1;0.739888,MA0149.1;0.769072,MA0062.2;0.353589,MA0035.2;0.778873,MA0039.2;1.13403,MA0138.2;0.928035,MA0002.2;0.379056,MA0137.2;0.558189,MA0104.2;0.392359,MA0047.2;0.856092,MA0112.2;5.79077,MA0065.2;1.7213,MA0150.1;0.633493,MA0151.1;0,MA0152.1;0.78681,MA0153.1;1.30799,MA0154.1;0.229241,MA0155.1;0.180766,MA0156.1;0.560797,MA0157.1;0.97481,MA0158.1;0,MA0159.1;0.462502,MA0160.1;0.756582,MA0161.1;0,MA0162.1;4.24646,MA0163.1;3.14178,MA0164.1;0.90014,MA0080.2;0.535868,MA0018.2;0.870662,MA0099.2;0.7872,MA0079.2;2.72671,MA0102.2;1.75932,MA0258.1;3.84649,MA0259.1;0.471671,MA0442.1;0}}
|full_id=C2071_Dendritic_Endothelial_Renal_Hepatic_immature_Lymphatic_brain
|id=C2071
|ontology_enrichment_celltype=CL:0000115!3.26e-17!35;CL:0002139!6.76e-16!24;CL:0002078!1.78e-12!44;CL:0000071!5.93e-12!18;CL:0002546!5.93e-12!18;CL:0000213!2.23e-11!57;CL:0000215!2.23e-11!57
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0007023!2.42e-25!115;UBERON:0005743!6.96e-24!86;UBERON:0002346!2.58e-23!90;UBERON:0000073!4.11e-23!94;UBERON:0001016!4.11e-23!94;UBERON:0001049!9.13e-23!57;UBERON:0005068!9.13e-23!57;UBERON:0006241!9.13e-23!57;UBERON:0007135!9.13e-23!57;UBERON:0003075!1.27e-22!86;UBERON:0007284!1.27e-22!86;UBERON:0001017!4.04e-22!82;UBERON:0002616!1.14e-19!59;UBERON:0000955!2.21e-18!69;UBERON:0006238!2.21e-18!69;UBERON:0002780!2.78e-16!41;UBERON:0001890!2.78e-16!41;UBERON:0006240!2.78e-16!41;UBERON:0003080!4.00e-16!42;UBERON:0003056!5.01e-16!61;UBERON:0001893!2.28e-14!34;UBERON:0002020!3.23e-14!34;UBERON:0003528!3.23e-14!34;UBERON:0002791!6.58e-14!33;UBERON:0001869!2.98e-13!32;UBERON:0000025!2.80e-12!194;UBERON:0000153!4.39e-12!129;UBERON:0007811!4.39e-12!129;UBERON:0000033!5.25e-12!123;UBERON:0001986!5.93e-12!18;UBERON:0004638!5.93e-12!18;UBERON:0004852!5.93e-12!18;UBERON:0000924!1.07e-11!173;UBERON:0006601!1.07e-11!173;UBERON:0004111!2.33e-11!241;UBERON:0004121!4.50e-11!169;UBERON:0000487!4.45e-10!22;UBERON:0000956!7.63e-10!25;UBERON:0000203!7.63e-10!25;UBERON:0000477!1.27e-09!286;UBERON:0002619!4.85e-09!22;UBERON:0006914!6.25e-09!25;UBERON:0000119!2.96e-08!312;UBERON:0001950!3.55e-08!20;UBERON:0003076!6.48e-08!15;UBERON:0003057!6.48e-08!15;UBERON:0000483!8.09e-08!309;UBERON:0004732!8.71e-07!13
}}

Latest revision as of 11:58, 17 September 2013


Full id: C2071_Dendritic_Endothelial_Renal_Hepatic_immature_Lymphatic_brain



Phase1 CAGE Peaks

Hg19::chr10:72238517..72238595,+p1@KIAA1274
Hg19::chr10:72238698..72238712,+p4@KIAA1274
Hg19::chr10:72238717..72238746,+p2@KIAA1274
Hg19::chr10:72238747..72238760,+p3@KIAA1274


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>

Uber Anatomy
Ontology termp-valuen
adult organism1.60e-25114
neurectoderm2.34e-2286
neural plate5.81e-2282
presumptive neural plate5.81e-2282
neural tube5.41e-2056
neural rod5.41e-2056
future spinal cord5.41e-2056
neural keel5.41e-2056
central nervous system2.33e-1981
regional part of nervous system6.86e-1953
regional part of brain6.86e-1953
nervous system5.41e-1889
brain3.38e-1668
future brain3.38e-1668
pre-chordal neural plate1.56e-1561
anatomical cluster2.52e-15373
regional part of forebrain7.81e-1441
forebrain7.81e-1441
anterior neural tube7.81e-1441
future forebrain7.81e-1441
structure with developmental contribution from neural crest1.54e-13132
ecto-epithelium3.11e-13104
blood vessel endothelium3.78e-1318
endothelium3.78e-1318
cardiovascular system endothelium3.78e-1318
tube4.16e-12192
telencephalon4.51e-1234
brain grey matter1.04e-1134
gray matter1.04e-1134
simple squamous epithelium1.52e-1122
anatomical conduit2.32e-11240
cerebral hemisphere3.94e-1132
regional part of telencephalon4.68e-1132
squamous epithelium6.29e-1025
ectoderm-derived structure1.89e-09171
ectoderm1.89e-09171
presumptive ectoderm1.89e-09171
organ system subdivision1.42e-08223
cerebral cortex1.27e-0725
pallium1.27e-0725
posterior neural tube1.61e-0715
chordal neural plate1.61e-0715
cell layer2.35e-07309
epithelium6.06e-07306
organ part6.08e-07218


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)
MA0003.13.49532
MA0004.10.71247
MA0006.11.31813
MA0007.10.6918
MA0009.11.20602
MA0014.19.60141
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
MA0038.13.20044
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
MA0055.10.791759
MA0056.10
MA0057.10.248209
MA0058.10.605914
MA0059.10.604454
MA0060.12.70115
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
MA0073.10.866596
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
MA0105.10.232357
MA0106.10.869173
MA0107.10.453492
MA0108.21.03412
MA0109.10
MA0111.10.655276
MA0113.10.886811
MA0114.11.13665
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
MA0139.10.344952
MA0140.10.779643
MA0141.10.602484
MA0142.11.00381
MA0143.10.887001
MA0144.10.430413
MA0145.11.08195
MA0146.11.25938
MA0147.10.46175
MA0148.10.739888
MA0149.10.769072
MA0062.20.353589
MA0035.20.778873
MA0039.21.13403
MA0138.20.928035
MA0002.20.379056
MA0137.20.558189
MA0104.20.392359
MA0047.20.856092
MA0112.25.79077
MA0065.21.7213
MA0150.10.633493
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.10.229241
MA0155.10.180766
MA0156.10.560797
MA0157.10.97481
MA0158.10
MA0159.10.462502
MA0160.10.756582
MA0161.10
MA0162.14.24646
MA0163.13.14178
MA0164.10.90014
MA0080.20.535868
MA0018.20.870662
MA0099.20.7872
MA0079.22.72671
MA0102.21.75932
MA0258.13.84649
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
EBF1#187948.9064668465690.00015887907472010.00199317377593904
EGR1#195844.988179094810140.001615011500076050.0101242608677337
MYC#460945.22228187160940.001344309395272740.00885458683986436
PBX3#5090421.91451268674414.33289161192893e-060.000135892752870344
ZBTB7A#5134147.35190930787590.000342223540015990.0034582955293401
ZNF263#1012748.221841637010680.0002187871180958320.00248045026344014



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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