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Coexpression cluster:C1403: Difference between revisions

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{{Coexpression_clusters
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,0.417013,0.00857271,0.21822,0.388558,0.397562,0.21727,0.351946,0.345508,0.484083,0.00484044,0.0207403,0.302171,0.398223,0.178399,0.547908,0.400541,0.372405,0.182559,0.164471,0.00770234,0.313891,3.09948e-05,0.00405216,0.137165,4.56472e-06,0.191837,0.395568,0.320916,0.289812,0.384881,0.00303043,0.369492,0.592234|tfbs_overrepresentation_for_novel_motifs=0.44418,1.35536,0.436508,0.58616,0.393082,0.584466,0.662701,0.269608,0.267027,3.20111,0.553339,0.707204,1.18908,1.56773,0.391663,0.415981,0.889639,0.336106,0.236034,0.127969,0.436569,0.0880431,0.576478,0.387783,0.483957,0.730467,0.202389,0.574247,0.396295,0.186644,0.530785,0.92701,0.816912,2.62317,0.35719,2.26978,0.93226,0.585658,0.329602,0.248856,0.355745,0.513952,0.664116,0.390088,0.354447,0.468392,1.59472,2.29967,0.304272,1.02586,0.745008,0.675919,0.149032,1.00488,1.15929,0.653901,0.400834,1.50361,0.186533,0.619193,0.968558,1.59978,0.267534,0.861462,0.684675,0.826413,1.24834,1.61834,0.916468,1.45553,0.500342,0.275507,16.9753,1.15727,1.17153,1.75965,0.192925,1.96776,0.913168,1.20149,0.240887,0.86037,0.684313,0.272514,1.10535,1.10459,4.85059,0.536262,0.771626,1.71797,1.34233,1.07807,0.94406,0.30974,7.09564,0.32338,0.234532,0.987239,0.776336,2.19258,0.330999,0.938327,0.981588,0.893363,0.814675,2.321,0.877269,0.647343,10.718,0.376529,1.13818,0.978783,0.430775,0.563054,1.29401,0.352243,1.70375,2.25836,0.824029,0.312699,1.14892,0.769145,0.581628,0.695878,1.40534,0.845034,0.656181,0.949126,1.1919,0.324369,1.07876,0.53374,1.20639,2.78399,1.35529,0.999497,0.524606,0.57483,1.31259,2.17352,1.7705,1.27501,0.657956,0.983666,0.816466,0.611524,0.799467,2.01411,0.510514,0.306342,0.424432,5.86295,1.07915,0.717973,0.665754,1.48627,0.755083,0.378604,0.484017,0.454152,1.27379,1.06043,0.912368,1.1583,0.83286,0.683502,1.45122,1.58953,0.0115686|tfbs_overrepresentation_jaspar=MA0003.1;0.0799681,MA0004.1;0.558729,MA0006.1;1.01439,MA0007.1;0.539222,MA0009.1;1.03681,MA0014.1;2.54844,MA0017.1;0.432438,MA0019.1;0.7124,MA0024.1;2.14259,MA0025.1;1.17262,MA0027.1;2.65688,MA0028.1;1.85223,MA0029.1;0.949428,MA0030.1;0.937696,MA0031.1;0.871496,MA0038.1;0.665566,MA0040.1;0.955415,MA0041.1;0.578072,MA0042.1;0.544748,MA0043.1;2.36158,MA0046.1;1.02569,MA0048.1;0.152639,MA0050.1;0.545671,MA0051.1;0.661179,MA0052.1;0.959373,MA0055.1;0.0586456,MA0056.1;0,MA0057.1;9.04743,MA0058.1;0.458909,MA0059.1;0.457555,MA0060.1;1.35477,MA0061.1;1.93637,MA0063.1;0,MA0066.1;0.66601,MA0067.1;1.35893,MA0068.1;0.199491,MA0069.1;1.02175,MA0070.1;1.01032,MA0071.1;0.625297,MA0072.1;1.00572,MA0073.1;66.38,MA0074.1;0.660398,MA0076.1;4.17659,MA0077.1;0.997832,MA0078.1;0.763954,MA0081.1;0.457725,MA0083.1;1.04447,MA0084.1;1.5477,MA0087.1;1.00322,MA0088.1;1.09824,MA0089.1;0,MA0090.1;0.490736,MA0091.1;0.561458,MA0092.1;0.522012,MA0093.1;0.394379,MA0095.1;0,MA0098.1;0,MA0100.1;0.679972,MA0101.1;1.02896,MA0103.1;0.381434,MA0105.1;0.134725,MA0106.1;0.70837,MA0107.1;0.857383,MA0108.2;0.868347,MA0109.1;0,MA0111.1;0.504913,MA0113.1;0.725375,MA0114.1;0.314898,MA0115.1;1.28169,MA0116.1;0.323925,MA0117.1;1.07516,MA0119.1;0.440684,MA0122.1;1.10154,MA0124.1;1.23968,MA0125.1;1.15445,MA0130.1;0,MA0131.1;0.782708,MA0132.1;0,MA0133.1;0,MA0135.1;1.06778,MA0136.1;0.672893,MA0139.1;0.226048,MA0140.1;0.622527,MA0141.1;0.455728,MA0142.1;0.838805,MA0143.1;1.72302,MA0144.1;0.299851,MA0145.1;1.16614,MA0146.1;0.232472,MA0147.1;0.327615,MA0148.1;0.584698,MA0149.1;0.612449,MA0062.2;3.52102,MA0035.2;0.621793,MA0039.2;0.569061,MA0138.2;0.765223,MA0002.2;0.255126,MA0137.2;0.414885,MA0104.2;0.26661,MA0047.2;0.695777,MA0112.2;0.680553,MA0065.2;0.109623,MA0150.1;0.484557,MA0151.1;0,MA0152.1;0.629368,MA0153.1;1.13732,MA0154.1;0.819655,MA0155.1;0.0961854,MA0156.1;2.81343,MA0157.1;0.810597,MA0158.1;0,MA0159.1;2.38949,MA0160.1;0.600559,MA0161.1;0,MA0162.1;1.39622,MA0163.1;8.88651,MA0164.1;0.738243,MA0080.2;0.394469,MA0018.2;0.709805,MA0099.2;0.629739,MA0079.2;40.5706,MA0102.2;1.58513,MA0258.1;0.289793,MA0259.1;0.336472,MA0442.1;0}}
|full_id=C1403_occipital_Fibroblast_parietal_normal_duodenum_temporal_Neurons
|id=C1403
}}

Latest revision as of 11:44, 17 September 2013


Full id: C1403_occipital_Fibroblast_parietal_normal_duodenum_temporal_Neurons



Phase1 CAGE Peaks

Hg19::chr15:37392534..37392562,-p10@MEIS2
Hg19::chr15:37392576..37392589,-p12@MEIS2
Hg19::chr15:37392593..37392607,-p13@MEIS2
Hg19::chr15:37392616..37392638,-p2@MEIS2
Hg19::chr15:37392703..37392717,-p8@MEIS2
Hg19::chr15:37392724..37392757,-p1@MEIS2


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
skin fibroblast4.40e-0723
fibroblast5.16e-0776
Uber Anatomy
Ontology termp-valuen
anatomical cluster8.31e-19373
anatomical conduit3.32e-17240
structure with developmental contribution from neural crest2.83e-16132
tube3.29e-15192
neural plate6.45e-1582
presumptive neural plate6.45e-1582
central nervous system6.85e-1581
neurectoderm8.51e-1586
nervous system8.68e-1589
multi-tissue structure1.14e-14342
neural tube5.04e-1456
neural rod5.04e-1456
future spinal cord5.04e-1456
neural keel5.04e-1456
brain1.72e-1368
future brain1.72e-1368
regional part of nervous system2.99e-1353
regional part of brain2.99e-1353
organ system subdivision5.93e-13223
epithelium1.04e-12306
brain grey matter2.26e-1234
gray matter2.26e-1234
cerebral hemisphere7.42e-1232
cell layer8.27e-12309
regional part of forebrain8.59e-1241
forebrain8.59e-1241
anterior neural tube8.59e-1241
future forebrain8.59e-1241
regional part of telencephalon1.25e-1132
telencephalon1.60e-1134
adult organism2.68e-11114
ectoderm-derived structure7.22e-11171
ectoderm7.22e-11171
presumptive ectoderm7.22e-11171
pre-chordal neural plate7.97e-1161
multi-cellular organism1.74e-10656
anatomical system5.01e-10624
anatomical group5.08e-10625
ecto-epithelium1.14e-09104
organ2.78e-09503
cerebral cortex5.59e-0925
pallium5.59e-0925
regional part of cerebral cortex2.15e-0722
organ part3.14e-07218
neocortex4.38e-0720


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)
MA0003.10.0799681
MA0004.10.558729
MA0006.11.01439
MA0007.10.539222
MA0009.11.03681
MA0014.12.54844
MA0017.10.432438
MA0019.10.7124
MA0024.12.14259
MA0025.11.17262
MA0027.12.65688
MA0028.11.85223
MA0029.10.949428
MA0030.10.937696
MA0031.10.871496
MA0038.10.665566
MA0040.10.955415
MA0041.10.578072
MA0042.10.544748
MA0043.12.36158
MA0046.11.02569
MA0048.10.152639
MA0050.10.545671
MA0051.10.661179
MA0052.10.959373
MA0055.10.0586456
MA0056.10
MA0057.19.04743
MA0058.10.458909
MA0059.10.457555
MA0060.11.35477
MA0061.11.93637
MA0063.10
MA0066.10.66601
MA0067.11.35893
MA0068.10.199491
MA0069.11.02175
MA0070.11.01032
MA0071.10.625297
MA0072.11.00572
MA0073.166.38
MA0074.10.660398
MA0076.14.17659
MA0077.10.997832
MA0078.10.763954
MA0081.10.457725
MA0083.11.04447
MA0084.11.5477
MA0087.11.00322
MA0088.11.09824
MA0089.10
MA0090.10.490736
MA0091.10.561458
MA0092.10.522012
MA0093.10.394379
MA0095.10
MA0098.10
MA0100.10.679972
MA0101.11.02896
MA0103.10.381434
MA0105.10.134725
MA0106.10.70837
MA0107.10.857383
MA0108.20.868347
MA0109.10
MA0111.10.504913
MA0113.10.725375
MA0114.10.314898
MA0115.11.28169
MA0116.10.323925
MA0117.11.07516
MA0119.10.440684
MA0122.11.10154
MA0124.11.23968
MA0125.11.15445
MA0130.10
MA0131.10.782708
MA0132.10
MA0133.10
MA0135.11.06778
MA0136.10.672893
MA0139.10.226048
MA0140.10.622527
MA0141.10.455728
MA0142.10.838805
MA0143.11.72302
MA0144.10.299851
MA0145.11.16614
MA0146.10.232472
MA0147.10.327615
MA0148.10.584698
MA0149.10.612449
MA0062.23.52102
MA0035.20.621793
MA0039.20.569061
MA0138.20.765223
MA0002.20.255126
MA0137.20.414885
MA0104.20.26661
MA0047.20.695777
MA0112.20.680553
MA0065.20.109623
MA0150.10.484557
MA0151.10
MA0152.10.629368
MA0153.11.13732
MA0154.10.819655
MA0155.10.0961854
MA0156.12.81343
MA0157.10.810597
MA0158.10
MA0159.12.38949
MA0160.10.600559
MA0161.10
MA0162.11.39622
MA0163.18.88651
MA0164.10.738243
MA0080.20.394469
MA0018.20.709805
MA0099.20.629739
MA0079.240.5706
MA0102.21.58513
MA0258.10.289793
MA0259.10.336472
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
CHD2#1106610.34402283411698.15706268702999e-073.55112742797301e-05
CTBP2#1488662.71700033932811.6349770986689e-111.99015586489372e-09
E2F1#186964.907389214879327.15746523583771e-050.00112696896090103
E2F6#187665.017155731697396.26776799983417e-050.00102473297140683
ELF1#199764.258097958807540.0001677224776288830.00205234538266935
EP300#203366.77394172622321.03454107484288e-050.000269509691482952
GABPB1#255367.067683836182178.01905956107035e-060.000222858584752162
HEY1#2346264.040111043105710.0002298968555807510.00253165306832539
MAFK#7975313.5503665689150.0009234722515590660.0067130589879987
MYC#460965.22228187160944.92821127172503e-050.000853844487404928
NFKB1#479065.488063424193843.65870229532191e-050.000707220449789237
NRF1#4899612.21027944771093.01474934717981e-071.51884904520074e-05
POLR2A#543062.147453176558070.01019570676818780.0380174022336666
REST#597869.650028716128021.23743801704917e-064.98791158095711e-05
SMARCB1#6598618.25271578115742.70039220880305e-081.85543593352093e-06
TAF1#687263.343046285745290.0007162474284635620.00573036350400689
TBP#690863.706770687096390.000385416472907960.00377709590072576
TCF7L2#6934610.77017656313736.40204410218762e-072.91212144594239e-05
YY1#752864.911170749853867.12445972864136e-050.00112380524029539
ZZZ3#260094159.6088082901554.50028907399422e-093.63781494271581e-07



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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