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{{Coexpression_clusters
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200105,0.227491,0.0497481,0.00335066,0.177664,0.28365,0.264413,0.131761,0.160658,0.206239,0.19924,0.28689,0.236464,0.325148,0.115817,0.00206474,0.223831,0.11528,0.0203812,0.190993,0.281727,0.283218,0.249955,0.164638,0.224257,0.0935776,0.327622,0.225752,0.207791,0.0958756,0.0859274,0.316866,0.171683,0.158847,0.271275,0.071111,0.270604,0.101021,0.222548,0.175934,0.157274,0.215705,0.252796,0.205954,0.361435|tfbs_overrepresentation_for_novel_motifs=1.66899,2.70919,0.690871,0.855819,0.641468,0.853988,0.937929,0.494933,0.491742,0.221898,0.820209,0.985163,0.436625,0.925331,0.639839,0.667627,1.17594,0.575162,0.452865,0.305559,0.69094,0.242883,0.845342,0.635379,0.743951,1.00973,0.409304,0.842925,0.645155,1.78451,0.795576,1.21459,0.534793,0.439574,1.46099,0.427404,0.596053,0.855276,0.567465,0.469078,1.45745,0.777097,0.718382,0.63803,0.151453,0.726632,0.939121,0.808003,0.69206,0.645308,1.02504,0.951993,0.893117,1.29475,1.45259,0.928548,0.650353,0.892517,1.0078,0.891404,1.25741,0.941709,0.492369,1.14672,0.961293,1.11026,1.54311,1.91674,1.2037,1.75271,0.762094,0.502203,0.886337,1.45054,1.10051,0.414196,0.396746,1.12884,1.20029,0.73687,0.459024,1.14559,0.960908,0.498519,1.39759,3.76231,1.48681,0.381882,1.053,2.0169,1.63834,1.36973,1.23218,0.543775,0.642354,0.560075,1.14422,1.27663,2.40384,0.946807,1.39614,1.22626,1.27082,2.65084,1.09802,0.815119,1.16312,0.921547,0.743661,1.50815,0.703975,1.26794,1.63757,0.830777,1.58942,0.594137,0.188952,0.794219,1.10778,0.547323,1.44203,1.0504,0.850918,0.973172,1.70203,1.12965,0.930979,1.2374,1.48578,0.561252,1.37044,0.798812,1.50051,0.969553,1.65144,0.372828,0.788803,0.843556,1.60823,2.47382,2.06967,1.57016,0.932872,1.27296,1.09989,0.883164,1.08214,2.31409,0.773313,0.539692,0.318511,2.79286,1.37083,3.10872,3.56276,1.78371,1.03563,2.5677,0.744018,0.710709,1.56892,1.35169,1.19946,0.714443,1.11698,0.960047,0.524529,0.936473,1.96295|tfbs_overrepresentation_jaspar=MA0003.1;5.30359,MA0004.1;0.826076,MA0006.1;1.5435,MA0007.1;0.804807,MA0009.1;1.3275,MA0014.1;0.758317,MA0017.1;0.686276,MA0019.1;0.990656,MA0024.1;2.72668,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;1.59304,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;4.54482,MA0074.1;0.935474,MA0076.1;0.734647,MA0077.1;2.86846,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;3.60951,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;1.06461,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;1.37817,MA0146.1;2.3244,MA0147.1;0.565108,MA0148.1;0.854239,MA0149.1;0.884158,MA0062.2;0.449458,MA0035.2;0.894194,MA0039.2;1.62945,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;0.277623,MA0150.1;0.744617,MA0151.1;0,MA0152.1;0.902317,MA0153.1;1.43021,MA0154.1;2.30945,MA0155.1;0.256269,MA0156.1;0.669101,MA0157.1;1.09377,MA0158.1;0,MA0159.1;0.565904,MA0160.1;0.871361,MA0161.1;0,MA0162.1;1.43223,MA0163.1;0.122425,MA0164.1;1.01792,MA0080.2;0.643061,MA0018.2;0.987913,MA0099.2;0.902716,MA0079.2;6.30148,MA0102.2;1.88331,MA0258.1;0.519674,MA0259.1;0.575594,MA0442.1;0}}
|full_id=C4786_occipital_H9_parietal_Neural_duodenum_Neurons_temporal
|id=C4786
|ontology_enrichment_celltype=CL:0002139!1.63e-10!24;CL:0002319!3.46e-10!25;CL:0002321!4.55e-10!248;CL:0000133!7.57e-10!59;CL:0000220!2.07e-09!246;CL:0000115!9.18e-09!35;CL:0002078!5.80e-08!44;CL:0000055!7.81e-08!180;CL:0000071!1.27e-07!18;CL:0002546!1.27e-07!18;CL:0000213!4.81e-07!57;CL:0000215!4.81e-07!57;CL:0000221!6.45e-07!71;CL:0000333!7.27e-07!41;CL:0000047!9.95e-07!8
|ontology_enrichment_disease=DOID:3095!4.47e-11!22;DOID:2994!4.47e-11!22
|ontology_enrichment_uberon=UBERON:0000073!9.76e-34!94;UBERON:0001016!9.76e-34!94;UBERON:0005743!1.37e-30!86;UBERON:0001017!1.77e-29!82;UBERON:0001049!7.48e-23!57;UBERON:0005068!7.48e-23!57;UBERON:0006241!7.48e-23!57;UBERON:0007135!7.48e-23!57;UBERON:0000955!9.61e-23!69;UBERON:0006238!9.61e-23!69;UBERON:0002346!1.33e-22!90;UBERON:0003075!4.98e-21!86;UBERON:0007284!4.98e-21!86;UBERON:0000924!2.88e-20!173;UBERON:0006601!2.88e-20!173;UBERON:0003056!2.82e-19!61;UBERON:0002616!4.17e-19!59;UBERON:0004121!6.97e-19!169;UBERON:0000025!1.36e-18!194;UBERON:0001893!1.75e-18!34;UBERON:0002020!1.84e-18!34;UBERON:0003528!1.84e-18!34;UBERON:0000119!3.05e-18!312;UBERON:0002780!3.53e-18!41;UBERON:0001890!3.53e-18!41;UBERON:0006240!3.53e-18!41;UBERON:0003080!4.51e-18!42;UBERON:0002791!5.99e-18!33;UBERON:0000483!7.10e-18!309;UBERON:0001869!3.17e-17!32;UBERON:0004111!8.53e-16!241;UBERON:0000033!1.29e-15!123;UBERON:0000153!5.91e-15!129;UBERON:0007811!5.91e-15!129;UBERON:0000956!2.52e-13!25;UBERON:0000203!2.52e-13!25;UBERON:0000475!1.37e-12!365;UBERON:0000477!2.17e-12!286;UBERON:0002619!4.09e-12!22;UBERON:0001950!4.32e-11!20;UBERON:0000468!4.63e-09!659;UBERON:0001986!1.27e-07!18;UBERON:0004638!1.27e-07!18;UBERON:0004852!1.27e-07!18;UBERON:0000922!1.89e-07!612;UBERON:0000064!2.29e-07!219;UBERON:0002049!5.57e-07!79;UBERON:0007798!5.57e-07!79
}}

Latest revision as of 14:19, 17 September 2013


Full id: C4786_occipital_H9_parietal_Neural_duodenum_Neurons_temporal



Phase1 CAGE Peaks

Hg19::chr9:103235365..103235419,+p1@TMEFF1
Hg19::chr9:103235423..103235444,+p4@TMEFF1
Hg19::chr9:103235453..103235470,+p3@TMEFF1


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>

Uber Anatomy
Ontology termp-valuen
nervous system1.61e-3589
central nervous system2.56e-3281
neurectoderm1.11e-2786
neural tube7.11e-2656
neural rod7.11e-2656
future spinal cord7.11e-2656
neural keel7.11e-2656
neural plate7.71e-2682
presumptive neural plate7.71e-2682
brain9.48e-2568
future brain9.48e-2568
regional part of nervous system6.27e-2453
regional part of brain6.27e-2453
pre-chordal neural plate3.58e-2261
ectoderm-derived structure6.08e-22171
ectoderm6.08e-22171
presumptive ectoderm6.08e-22171
telencephalon8.04e-2134
brain grey matter9.06e-2134
gray matter9.06e-2134
regional part of forebrain1.01e-1941
forebrain1.01e-1941
anterior neural tube1.01e-1941
future forebrain1.01e-1941
anatomical cluster1.32e-19373
ecto-epithelium1.35e-19104
regional part of telencephalon2.09e-1932
cerebral hemisphere2.40e-1932
structure with developmental contribution from neural crest2.42e-17132
tube8.03e-15192
cerebral cortex1.02e-1425
pallium1.02e-1425
cell layer2.42e-13309
regional part of cerebral cortex3.02e-1322
epithelium5.80e-13306
anatomical conduit9.69e-13240
neocortex3.97e-1220
organ system subdivision6.45e-10223
blood vessel endothelium1.14e-0818
endothelium1.14e-0818
cardiovascular system endothelium1.14e-0818
multi-cellular organism1.16e-08656
neural nucleus1.37e-079
nucleus of brain1.37e-079
posterior neural tube2.39e-0715
chordal neural plate2.39e-0715
basal ganglion5.09e-079
nuclear complex of neuraxis5.09e-079
aggregate regional part of brain5.09e-079
collection of basal ganglia5.09e-079
cerebral subcortex5.09e-079
organ part7.38e-07218
Disease
Ontology termp-valuen
germ cell and embryonal cancer7.65e-1222
germ cell cancer7.65e-1222
neuroectodermal tumor8.24e-0710


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)
MA0003.15.30359
MA0004.10.826076
MA0006.11.5435
MA0007.10.804807
MA0009.11.3275
MA0014.10.758317
MA0017.10.686276
MA0019.10.990656
MA0024.12.72668
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
MA0057.11.59304
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
MA0073.14.54482
MA0074.10.935474
MA0076.10.734647
MA0077.12.86846
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
MA0100.13.60951
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
MA0131.11.06461
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
MA0145.11.37817
MA0146.12.3244
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.21.62945
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.20.491226
MA0047.20.973066
MA0112.20.731309
MA0065.20.277623
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.12.30945
MA0155.10.256269
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.11.43223
MA0163.10.122425
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.26.30148
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
CTCF#1066435.360256373075030.0064925092527670.0281602713505434
E2F6#187635.017155731697390.00791769806886330.0324688420219104
EGR1#195834.988179094810140.008056488137383440.0322800416089998
MAX#414936.452555509007120.003721913834265510.0187548470007167
RAD21#5885310.35503389545630.0009004912073565420.0066917889003209
USF1#739136.361499277207960.00388404057290560.0191324079517823
ZBTB7A#5134137.35190930787590.002516255860282270.0141075394992495



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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