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Coexpression cluster:C990: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=0.348717,0.600139,0.905112,1.21028,0.301904,0.480078,1.36559,0.561282,0.190005,0.355088,0.450635,1.45571,0.907465,0.543352,0.81316,0.322799,0.774423,0.698835,0.491486,0.264925,1.62225,0.180463,0.472508,0.29709,1.00212,0.619829,0.135503,0.470396,0.304828,0.122648,0.429397,0.810962,1.17878,0.469827,0.269459,0.339976,0.735464,0.481208,0.685417,0.174436,0.268162,0.413601,0.444349,0.299183,0.0775086,0.371118,0.555735,0.440085,0.186577,1.4915,0.63387,0.567337,0.639783,0.887323,1.03948,0.546236,0.831988,0.514077,0.388089,1.27736,0.85167,0.558065,0.190442,0.746929,0.575742,0.712797,1.12756,1.49516,0.800646,1.33315,0.400869,0.197328,0.304852,1.03748,0.149081,1.36791,0.401476,0.730167,0.797419,0.379656,0.167664,0.745864,0.575394,0.19474,0.986227,0.0220225,0.9432,0.118789,0.659621,1.59442,1.22073,0.959334,0.827657,0.644398,2.2627,0.672575,0.488357,0.87,0.664183,0.106284,0.246049,0.822041,0.864454,0.778061,0.701386,0.446229,0.762347,1.33446,1.00159,1.42617,0.92894,0.861701,0.336372,2.02714,1.17281,0.265019,1.199,0.428232,0.710479,0.229841,1.02923,0.657218,0.477387,0.586509,1.28328,0.730921,0.548418,0.83262,1.07171,1.25306,0.960022,0.432175,1.08604,1.42587,1.23359,0.113443,0.423593,0.470947,1.19123,2.04907,1.64679,1.15398,0.550118,0.866494,0.703126,0.505785,0.686615,1.88987,0.410382,0.224241,0.0833399,0.190235,0.960402,0.183004,0.557588,1.36372,0.643609,0.786331,0.385642,0.357927,1.15277,0.941964,0.796636,0.36101,0.71907,0.574616,0.611402,0.553354,0.0203307
|tfbs_overrepresentation_jaspar=MA0003.1;0.0264723,MA0004.1;0.455723,MA0006.1;0.300178,MA0007.1;0.437331,MA0009.1;0.918715,MA0014.1;0.473479,MA0017.1;0.337901,MA0019.1;0.602411,MA0024.1;0.813542,MA0025.1;1.05265,MA0027.1;2.5321,MA0028.1;0.315574,MA0029.1;0.832916,MA0030.1;0.821423,MA0031.1;0.756713,MA0038.1;1.3714,MA0040.1;0.838784,MA0041.1;0.474018,MA0042.1;0.442535,MA0043.1;0.919032,MA0046.1;0.90778,MA0048.1;0.316923,MA0050.1;0.443405,MA0051.1;0.553205,MA0052.1;0.842664,MA0055.1;0.283474,MA0056.1;0,MA0057.1;0.305162,MA0058.1;0.362328,MA0059.1;0.948176,MA0060.1;2.3723,MA0061.1;0.497495,MA0063.1;0,MA0066.1;0.557833,MA0067.1;1.23721,MA0068.1;0.133123,MA0069.1;3.44729,MA0070.1;0.892666,MA0071.1;0.518907,MA0072.1;0.888148,MA0073.1;4.12944,MA0074.1;2.33338,MA0076.1;0.377799,MA0077.1;0.880402,MA0078.1;1.57046,MA0081.1;0.361233,MA0083.1;0.926258,MA0084.1;1.42483,MA0087.1;0.885691,MA0088.1;0.770971,MA0089.1;0,MA0090.1;1.01596,MA0091.1;0.458301,MA0092.1;0.421159,MA0093.1;0.303084,MA0095.1;0,MA0098.1;0,MA0100.1;0.571227,MA0101.1;0.30624,MA0103.1;0.792149,MA0105.1;0.0818021,MA0106.1;0.59853,MA0107.1;0.236528,MA0108.2;0.753643,MA0109.1;0,MA0111.1;0.405141,MA0113.1;0.614917,MA0114.1;0.231781,MA0115.1;1.1606,MA0116.1;0.673701,MA0117.1;0.956472,MA0119.1;0.345493,MA0122.1;0.982472,MA0124.1;1.11898,MA0125.1;1.0347,MA0130.1;0,MA0131.1;0.670358,MA0132.1;0,MA0133.1;0,MA0135.1;0.949204,MA0136.1;0.564434,MA0139.1;0.155155,MA0140.1;2.21469,MA0141.1;0.359385,MA0142.1;0.724856,MA0143.1;0.615094,MA0144.1;0.623945,MA0145.1;0.220937,MA0146.1;0.113833,MA0147.1;0.243042,MA0148.1;0.480298,MA0149.1;0.506665,MA0062.2;0.161302,MA0035.2;1.28264,MA0039.2;0.644124,MA0138.2;0.653421,MA0002.2;0.179788,MA0137.2;0.321796,MA0104.2;0.189646,MA0047.2;0.586412,MA0112.2;0.0572179,MA0065.2;0.0631316,MA0150.1;0.386144,MA0151.1;0,MA0152.1;0.52279,MA0153.1;1.01778,MA0154.1;0.274121,MA0155.1;0.0535085,MA0156.1;0.323987,MA0157.1;0.697424,MA0158.1;0,MA0159.1;0.243637,MA0160.1;0.495355,MA0161.1;0,MA0162.1;0.194027,MA0163.1;0.141536,MA0164.1;0.627336,MA0080.2;0.303167,MA0018.2;0.599912,MA0099.2;0.523145,MA0079.2;2.23097,MA0102.2;1.46209,MA0258.1;0.209744,MA0259.1;0.25092,MA0442.1;0
}}
}}

Revision as of 19:36, 22 January 2013


Full id: C990_pineal_occipital_merkel_Lens_medial_parietal_middle



Phase1 CAGE Peaks

Hg19::chr11:124589340..124589351,+p@chr11:124589340..124589351
+
Hg19::chr12:57735480..57735493,-p9@R3HDM2
Hg19::chr9:77112225..77112238,+p2@RORB
Hg19::chr9:77112244..77112262,+p1@RORB
Hg19::chr9:77114317..77114328,-p3@ENST00000417576
Hg19::chr9:77114341..77114368,-p1@ENST00000417576
Hg19::chr9:77114385..77114400,-p2@ENST00000417576
Hg19::chr9:77302053..77302065,+p@chr9:77302053..77302065
+


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

GO IDGO nameFDR corrected p-value
GO:0042462eye photoreceptor cell development0.00918254698947879
GO:0001754eye photoreceptor cell differentiation0.00918254698947879
GO:0042461photoreceptor cell development0.00918254698947879
GO:0043193positive regulation of gene-specific transcription0.00918254698947879
GO:0046530photoreceptor cell differentiation0.00918254698947879
GO:0032583regulation of gene-specific transcription0.00918254698947879
GO:0048592eye morphogenesis0.0170497870118158
GO:0001654eye development0.0269598341411594
GO:0007423sensory organ development0.0438243772124945



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><br>uberon_data<br><br>

Uber Anatomy
Ontology termp-valuen
neural tube4.19e-5556
neural rod4.19e-5556
future spinal cord4.19e-5556
neural keel4.19e-5556
regional part of nervous system2.00e-5053
regional part of brain2.00e-5053
central nervous system2.87e-5081
regional part of forebrain1.73e-4941
forebrain1.73e-4941
anterior neural tube1.73e-4941
future forebrain1.73e-4941
nervous system5.51e-4889
neural plate7.75e-4882
presumptive neural plate7.75e-4882
brain1.38e-4768
future brain1.38e-4768
neurectoderm4.05e-4786
pre-chordal neural plate1.41e-4561
adult organism6.01e-43114
telencephalon9.26e-4134
brain grey matter2.89e-4034
gray matter2.89e-4034
neocortex4.25e-3820
ecto-epithelium4.94e-38104
cerebral hemisphere8.49e-3832
regional part of cerebral cortex1.07e-3722
regional part of telencephalon2.27e-3732
cerebral cortex1.55e-3225
pallium1.55e-3225
ectoderm-derived structure1.21e-31171
ectoderm1.21e-31171
presumptive ectoderm1.21e-31171
structure with developmental contribution from neural crest1.75e-29132
organ system subdivision2.30e-17223
gyrus1.85e-136
occipital lobe1.24e-115
anatomical cluster1.24e-11373
tube1.47e-11192
parietal lobe2.04e-115
temporal lobe8.89e-116
anatomical conduit8.95e-11240
epithelium3.27e-10306
diencephalon5.82e-107
future diencephalon5.82e-107
cell layer5.85e-10309
basal ganglion1.36e-099
nuclear complex of neuraxis1.36e-099
aggregate regional part of brain1.36e-099
collection of basal ganglia1.36e-099
cerebral subcortex1.36e-099
neural nucleus3.13e-099
nucleus of brain3.13e-099
regional part of diencephalon1.09e-084
embryo1.09e-08592
multi-tissue structure2.11e-08342
posterior neural tube3.98e-0815
chordal neural plate3.98e-0815
multi-cellular organism4.99e-08656
organ part5.42e-08218
embryonic structure9.65e-08564
frontal cortex1.64e-073
germ layer1.93e-07560
germ layer / neural crest1.93e-07560
embryonic tissue1.93e-07560
presumptive structure1.93e-07560
germ layer / neural crest derived structure1.93e-07560
epiblast (generic)1.93e-07560
developing anatomical structure2.63e-07581
organ2.71e-07503
brainstem3.08e-076
limbic system9.97e-075


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)
MA0003.10.0264723
MA0004.10.455723
MA0006.10.300178
MA0007.10.437331
MA0009.10.918715
MA0014.10.473479
MA0017.10.337901
MA0019.10.602411
MA0024.10.813542
MA0025.11.05265
MA0027.12.5321
MA0028.10.315574
MA0029.10.832916
MA0030.10.821423
MA0031.10.756713
MA0038.11.3714
MA0040.10.838784
MA0041.10.474018
MA0042.10.442535
MA0043.10.919032
MA0046.10.90778
MA0048.10.316923
MA0050.10.443405
MA0051.10.553205
MA0052.10.842664
MA0055.10.283474
MA0056.10
MA0057.10.305162
MA0058.10.362328
MA0059.10.948176
MA0060.12.3723
MA0061.10.497495
MA0063.10
MA0066.10.557833
MA0067.11.23721
MA0068.10.133123
MA0069.13.44729
MA0070.10.892666
MA0071.10.518907
MA0072.10.888148
MA0073.14.12944
MA0074.12.33338
MA0076.10.377799
MA0077.10.880402
MA0078.11.57046
MA0081.10.361233
MA0083.10.926258
MA0084.11.42483
MA0087.10.885691
MA0088.10.770971
MA0089.10
MA0090.11.01596
MA0091.10.458301
MA0092.10.421159
MA0093.10.303084
MA0095.10
MA0098.10
MA0100.10.571227
MA0101.10.30624
MA0103.10.792149
MA0105.10.0818021
MA0106.10.59853
MA0107.10.236528
MA0108.20.753643
MA0109.10
MA0111.10.405141
MA0113.10.614917
MA0114.10.231781
MA0115.11.1606
MA0116.10.673701
MA0117.10.956472
MA0119.10.345493
MA0122.10.982472
MA0124.11.11898
MA0125.11.0347
MA0130.10
MA0131.10.670358
MA0132.10
MA0133.10
MA0135.10.949204
MA0136.10.564434
MA0139.10.155155
MA0140.12.21469
MA0141.10.359385
MA0142.10.724856
MA0143.10.615094
MA0144.10.623945
MA0145.10.220937
MA0146.10.113833
MA0147.10.243042
MA0148.10.480298
MA0149.10.506665
MA0062.20.161302
MA0035.21.28264
MA0039.20.644124
MA0138.20.653421
MA0002.20.179788
MA0137.20.321796
MA0104.20.189646
MA0047.20.586412
MA0112.20.0572179
MA0065.20.0631316
MA0150.10.386144
MA0151.10
MA0152.10.52279
MA0153.11.01778
MA0154.10.274121
MA0155.10.0535085
MA0156.10.323987
MA0157.10.697424
MA0158.10
MA0159.10.243637
MA0160.10.495355
MA0161.10
MA0162.10.194027
MA0163.10.141536
MA0164.10.627336
MA0080.20.303167
MA0018.20.599912
MA0099.20.523145
MA0079.22.23097
MA0102.21.46209
MA0258.10.209744
MA0259.10.25092
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
ZNF263#1012755.138651023131670.001082531249033560.00764063533944823



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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