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Coexpression cluster:C2398: Difference between revisions

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{{Coexpression_clusters
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,0.259901,0.139723,0.0708274,0.0710478,0.196248,0.102645,0.0539258,0.0709978,0.401939,0.332746,0.271338,0.242121,0.298673,0.244395,0.106889,0.128632,0.0845989,0.159153,0.0842401,0.13698,0.0874421,0.100355,0.167854,0.142846,0.0583767,0.088258,0.117657,0.0486914,0.175784,0.262778,0.0805224,0.362662,0.00277084,0.184359,0.334474,0.325785,0.257476,0.291176,0.376537,0.322827,0.229571,0.359036,0.0641033,0.171704,0.208256,0.265058,0.256405,0.362898,0.302133,0.40806,0.151361,0.279606,0.286696,0.150674,0.251128,0.246177,0.35674,0.35852,0.318525,0.213257,0.287217,0.122782,0.410951,0.289049,0.266974,0.125746,0.112897,0.398354,0.222091,0.205977,0.34423,0.0936726,0.343425,0.132374,0.285122,0.22741,0.203996,0.276721,0.321965,0.264707,0.450113|tfbs_overrepresentation_for_novel_motifs=1.44014,1.54039,1.42265,0.741427,0.534346,0.739643,0.821651,0.395818,0.392841,2.07992,0.706765,0.867962,1.62243,0.809319,0.532789,0.559384,1.05593,0.471262,0.356737,0.635753,0.581762,0.975621,0.731221,0.528529,0.632849,0.892087,0.316693,0.728867,0.537869,1.46495,0.682839,1.09415,0.433165,0.911389,0.49475,0.0842336,1.23038,0.740899,0.463978,0.371755,0.493145,1.59701,0.539378,0.53106,0.314427,1.49501,0.822818,0.694903,0.173425,2.28614,0.90714,0.83543,1.99838,1.17354,1.33024,0.812467,0.54284,1.82985,0.806003,0.776148,1.13655,0.825354,0.393426,1.02706,0.844545,0.991076,1.42026,1.79268,1.08337,1.62905,2.64981,1.83352,0.248021,1.32819,5.3994,0.859396,0.305238,1.00941,1.08,0.62601,0.95118,1.02594,0.844168,0.399165,1.27559,3.76398,1.18341,0.291738,0.934646,1.89266,1.51507,1.24792,1.11156,0.441618,0.535192,1.15724,0.354969,1.15558,0.939507,0.272395,0.465545,1.1057,1.14983,1.05974,0.979006,1.67377,1.04326,0.805616,0.632569,0.516141,0.594299,1.14697,2.40834,0.717043,1.46636,0.489254,11.6029,0.681522,0.988625,0.444962,1.31973,0.932085,0.736652,0.856196,1.57854,1.0102,0.814847,1.11673,1.36323,0.458105,1.24863,0.68598,1.37788,0.852645,1.52813,0.283547,2.73245,0.729481,1.48509,2.34913,1.94535,1.44718,0.8167,1.15194,0.980848,0.768101,0.963351,2.1895,0.661255,1.95303,0.66252,1.00204,1.24902,0.383416,0.824835,1.65997,0.917558,0.518428,3.77839,0.600782,1.44595,1.23002,1.07918,0.604379,0.997702,0.843324,0.423521,0.820225,7.32654|tfbs_overrepresentation_jaspar=MA0003.1;1.05935,MA0004.1;0.71247,MA0006.1;0.532262,MA0007.1;0.6918,MA0009.1;1.20602,MA0014.1;1.86845,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;0.709734,MA0050.1;0.69864,MA0051.1;0.820063,MA0052.1;1.12718,MA0055.1;0.396851,MA0056.1;0,MA0057.1;0.248209,MA0058.1;0.605914,MA0059.1;0.604454,MA0060.1;0.393285,MA0061.1;1.68681,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;0.00636811,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;1.6149,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;1.1497,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;2.8366,MA0124.1;1.41151,MA0125.1;1.32534,MA0130.1;0,MA0131.1;2.17614,MA0132.1;0,MA0133.1;0,MA0135.1;1.23748,MA0136.1;0.832277,MA0139.1;4.40535,MA0140.1;0.779643,MA0141.1;0.602484,MA0142.1;1.00381,MA0143.1;0.887001,MA0144.1;2.87436,MA0145.1;1.08195,MA0146.1;5.02892,MA0147.1;0.46175,MA0148.1;0.739888,MA0149.1;0.769072,MA0062.2;0.353589,MA0035.2;0.778873,MA0039.2;0.0247757,MA0138.2;0.928035,MA0002.2;0.379056,MA0137.2;0.558189,MA0104.2;0.392359,MA0047.2;0.856092,MA0112.2;2.35508,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;1.02191,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;1.90765,MA0164.1;0.90014,MA0080.2;0.535868,MA0018.2;0.870662,MA0099.2;0.7872,MA0079.2;0.0270533,MA0102.2;1.75932,MA0258.1;0.418966,MA0259.1;0.471671,MA0442.1;0}}
|full_id=C2398_brain_occipital_parietal_temporal_cerebellum_globus_optic
|id=C2398
}}

Latest revision as of 12:04, 17 September 2013


Full id: C2398_brain_occipital_parietal_temporal_cerebellum_globus_optic



Phase1 CAGE Peaks

Hg19::chr17:27507377..27507391,-p4@MYO18A
Hg19::chr17:27507395..27507449,-p1@MYO18A
Hg19::chr17:27507450..27507461,-p5@MYO18A
Hg19::chr17:27507464..27507475,-p6@MYO18A


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
epithelial cell4.54e-13253
ectodermal cell7.34e-0772
Uber Anatomy
Ontology termp-valuen
ectoderm-derived structure1.34e-36171
ectoderm1.34e-36171
presumptive ectoderm1.34e-36171
central nervous system1.37e-3481
organ system subdivision8.15e-34223
ecto-epithelium8.84e-34104
neural tube9.82e-3256
neural rod9.82e-3256
future spinal cord9.82e-3256
neural keel9.82e-3256
brain3.10e-3168
future brain3.10e-3168
nervous system7.13e-3189
regional part of nervous system8.32e-3053
regional part of brain8.32e-3053
neural plate4.64e-2982
presumptive neural plate4.64e-2982
anatomical cluster6.33e-29373
neurectoderm2.93e-2886
multi-tissue structure8.39e-24342
organ part1.89e-22218
structure with developmental contribution from neural crest2.22e-22132
regional part of forebrain2.81e-2241
forebrain2.81e-2241
anterior neural tube2.81e-2241
future forebrain2.81e-2241
pre-chordal neural plate7.49e-2161
adult organism2.13e-20114
cell layer1.21e-19309
brain grey matter1.34e-1934
gray matter1.34e-1934
telencephalon1.53e-1934
epithelium1.58e-19306
organ1.70e-19503
cerebral hemisphere2.09e-1832
regional part of telencephalon2.25e-1832
anatomical conduit5.12e-18240
tube1.14e-16192
regional part of cerebral cortex4.77e-1522
cerebral cortex1.11e-1425
pallium1.11e-1425
neocortex7.40e-1420
multi-cellular organism9.86e-14656
anatomical system6.84e-13624
anatomical group8.51e-13625
posterior neural tube1.41e-1015
chordal neural plate1.41e-1015
embryo2.04e-09592
segmental subdivision of nervous system2.13e-0913
developing anatomical structure5.98e-09581
segmental subdivision of hindbrain9.06e-0912
hindbrain9.06e-0912
presumptive hindbrain9.06e-0912
endoderm-derived structure9.08e-09160
endoderm9.08e-09160
presumptive endoderm9.08e-09160
trunk region element1.78e-08101
digestive system1.06e-07145
digestive tract1.06e-07145
primitive gut1.06e-07145
primordium1.29e-07160
embryonic structure2.68e-07564
organ segment2.82e-0798
regional part of metencephalon4.48e-079
metencephalon4.48e-079
future metencephalon4.48e-079
germ layer5.44e-07560
germ layer / neural crest5.44e-07560
embryonic tissue5.44e-07560
presumptive structure5.44e-07560
germ layer / neural crest derived structure5.44e-07560
epiblast (generic)5.44e-07560


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)
MA0003.11.05935
MA0004.10.71247
MA0006.10.532262
MA0007.10.6918
MA0009.11.20602
MA0014.11.86845
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
MA0048.10.709734
MA0050.10.69864
MA0051.10.820063
MA0052.11.12718
MA0055.10.396851
MA0056.10
MA0057.10.248209
MA0058.10.605914
MA0059.10.604454
MA0060.10.393285
MA0061.11.68681
MA0063.10
MA0066.10.825101
MA0067.11.53181
MA0068.10.313194
MA0069.11.19071
MA0070.11.17908
MA0071.10.782546
MA0072.11.1744
MA0073.10.00636811
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
MA0092.11.6149
MA0093.10.535768
MA0095.10
MA0098.10
MA0100.10.83965
MA0101.10.539569
MA0103.10.521546
MA0105.10.232357
MA0106.10.869173
MA0107.11.1497
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
MA0122.12.8366
MA0124.11.41151
MA0125.11.32534
MA0130.10
MA0131.12.17614
MA0132.10
MA0133.10
MA0135.11.23748
MA0136.10.832277
MA0139.14.40535
MA0140.10.779643
MA0141.10.602484
MA0142.11.00381
MA0143.10.887001
MA0144.12.87436
MA0145.11.08195
MA0146.15.02892
MA0147.10.46175
MA0148.10.739888
MA0149.10.769072
MA0062.20.353589
MA0035.20.778873
MA0039.20.0247757
MA0138.20.928035
MA0002.20.379056
MA0137.20.558189
MA0104.20.392359
MA0047.20.856092
MA0112.22.35508
MA0065.20.199162
MA0150.10.633493
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.10.229241
MA0155.11.02191
MA0156.10.560797
MA0157.10.97481
MA0158.10
MA0159.10.462502
MA0160.10.756582
MA0161.10
MA0162.10.0928415
MA0163.11.90765
MA0164.10.90014
MA0080.20.535868
MA0018.20.870662
MA0099.20.7872
MA0079.20.0270533
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
BCLAF1#9774421.65264761012184.54636978835329e-060.000141567774098339
CCNT2#90546.336201576962630.0006203100587215640.00511847690786296
CTCF#1066445.360256373075030.001211145381643620.00816913023207687
CTCFL#140690419.74647435897446.5732084880439e-060.000192782735546986
E2F1#186944.907389214879320.001724022357361790.0106453335095488
E2F6#187645.017155731697390.00157802193473060.00996475197057434
EBF1#187948.9064668465690.00015887907472010.00199509098048485
ELF1#199744.258097958807540.003041525565781240.0160796703905151
GABPB1#255347.067683836182170.0004006876864423170.00390149368677504
HEY1#2346244.040111043105710.00375304636917980.0185888461420264
HMGN3#932448.178547723350590.0002234570284440470.00248035164137186
NRF1#4899412.21027944771094.49717228915276e-050.000793378676869637
PAX5#507946.669565531177830.0005052774169483260.00443674694372509
RAD21#5885410.35503389545638.6948481184721e-050.00129319459220323
SMARCB1#6598418.25271578115749.00423392720929e-060.00024125017627599
SMC3#9126415.04493284493281.95092670935632e-050.000437707485710988
SRF#6722413.79717826216782.75840773062708e-050.00058387787794682
TAF1#687243.343046285745290.008005664898701650.0321937405704633
TAF7#6879411.43306940492395.85061525419808e-050.000968355636344205
TBP#690843.706770687096390.005296377814784350.0243967892470455
TCF12#6938410.63446490218647.8163066689251e-050.00119995186270156
YY1#752844.911170749853860.00171871838055440.0106763355110165
ZBTB7A#5134147.35190930787590.000342223540015990.00346298656096599
ZNF143#7702413.50087655222793.00867915035614e-050.000620504426903722
ZNF263#1012748.221841637010680.0002187871180958320.00248665881236376
ZNF274#1078241421.746153846152.33614176794641e-133.50049225398214e-11



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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