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Coexpression cluster:C1067: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=0.348717,0.600139,0.341646,0.481684,0.301904,0.480078,0.554663,0.19223,0.190005,6.49426,0.450635,0.597407,0.152895,0.543352,0.300614,0.863056,0.774423,0.250594,1.51831,0.560708,0.341703,0.405031,0.472508,0.29709,1.77507,1.50277,0.135503,0.470396,0.304828,0.388322,0.429397,0.810962,1.17878,0.154814,1.36232,14.8947,0.266487,0.481208,0.244807,3.00164,0.268162,0.413601,0.775279,0.299183,0.198862,0.371118,0.555735,0.440085,0.186577,0.304949,0.63387,0.567337,0.309329,0.887323,1.03948,0.546236,0.308962,0.514077,0.388089,0.513089,1.98297,0.558065,0.190442,0.746929,0.575742,0.712797,1.12756,1.49516,0.800646,1.33315,0.400869,0.197328,0.0911419,1.03748,0.455523,1.97519,0.799673,0.730167,0.797419,0.379656,0.167664,2.95309,0.575394,0.19474,0.986227,1.47034,0.26222,1.81046,1.58596,1.59442,1.22073,0.959334,0.827657,0.227232,0.302606,1.9383,0.946574,0.87,0.664183,1.70117,0.246049,0.822041,0.864454,0.778061,0.701386,0.446229,0.762347,0.539961,0.385342,0.286892,0.352381,2.00355,0.336372,0.459808,1.17281,0.265019,5.1372,0.428232,0.710479,0.229841,1.02923,0.657218,0.477387,0.586509,1.28328,0.730921,0.548418,0.83262,1.07171,1.25306,0.960022,0.432175,1.08604,2.43348,1.23359,0.113443,2.84277,0.470947,1.19123,2.04907,1.64679,1.15398,0.550118,0.866494,0.703126,2.1801,0.686615,1.88987,0.410382,0.224241,1.48708,0.743411,0.960402,0.183004,0.557588,1.36372,0.643609,0.786331,0.385642,0.941217,1.15277,0.941964,0.796636,0.948033,0.71907,0.574616,1.15008,0.553354,0.00340764
|tfbs_overrepresentation_for_novel_motifs=0.348717,0.600139,0.341646,0.481684,0.301904,0.480078,0.554663,0.19223,0.190005,6.49426,0.450635,0.597407,0.152895,0.543352,0.300614,0.863056,0.774423,0.250594,1.51831,0.560708,0.341703,0.405031,0.472508,0.29709,1.77507,1.50277,0.135503,0.470396,0.304828,0.388322,0.429397,0.810962,1.17878,0.154814,1.36232,14.8947,0.266487,0.481208,0.244807,3.00164,0.268162,0.413601,0.775279,0.299183,0.198862,0.371118,0.555735,0.440085,0.186577,0.304949,0.63387,0.567337,0.309329,0.887323,1.03948,0.546236,0.308962,0.514077,0.388089,0.513089,1.98297,0.558065,0.190442,0.746929,0.575742,0.712797,1.12756,1.49516,0.800646,1.33315,0.400869,0.197328,0.0911419,1.03748,0.455523,1.97519,0.799673,0.730167,0.797419,0.379656,0.167664,2.95309,0.575394,0.19474,0.986227,1.47034,0.26222,1.81046,1.58596,1.59442,1.22073,0.959334,0.827657,0.227232,0.302606,1.9383,0.946574,0.87,0.664183,1.70117,0.246049,0.822041,0.864454,0.778061,0.701386,0.446229,0.762347,0.539961,0.385342,0.286892,0.352381,2.00355,0.336372,0.459808,1.17281,0.265019,5.1372,0.428232,0.710479,0.229841,1.02923,0.657218,0.477387,0.586509,1.28328,0.730921,0.548418,0.83262,1.07171,1.25306,0.960022,0.432175,1.08604,2.43348,1.23359,0.113443,2.84277,0.470947,1.19123,2.04907,1.64679,1.15398,0.550118,0.866494,0.703126,2.1801,0.686615,1.88987,0.410382,0.224241,1.48708,0.743411,0.960402,0.183004,0.557588,1.36372,0.643609,0.786331,0.385642,0.941217,1.15277,0.941964,0.796636,0.948033,0.71907,0.574616,1.15008,0.553354,0.00340764
|tfbs_overrepresentation_jaspar=MA0003.1;0.797136,MA0004.1;0.455723,MA0006.1;2.25059,MA0007.1;0.437331,MA0009.1;0.918715,MA0014.1;0.275152,MA0017.1;0.337901,MA0019.1;0.602411,MA0024.1;0.813542,MA0025.1;1.05265,MA0027.1;2.5321,MA0028.1;0.846854,MA0029.1;0.832916,MA0030.1;0.821423,MA0031.1;0.756713,MA0038.1;0.557409,MA0040.1;0.838784,MA0041.1;0.474018,MA0042.1;0.442535,MA0043.1;0.919032,MA0046.1;0.90778,MA0048.1;0.653157,MA0050.1;0.443405,MA0051.1;0.553205,MA0052.1;0.842664,MA0055.1;2.12623,MA0056.1;0,MA0057.1;0.305162,MA0058.1;0.362328,MA0059.1;0.361075,MA0060.1;0.190336,MA0061.1;0.165998,MA0063.1;0,MA0066.1;0.557833,MA0067.1;1.23721,MA0068.1;0.133123,MA0069.1;0.903908,MA0070.1;0.892666,MA0071.1;0.518907,MA0072.1;0.888148,MA0073.1;0.000871324,MA0074.1;0.552456,MA0076.1;0.377799,MA0077.1;0.880402,MA0078.1;0.652193,MA0081.1;2.54896,MA0083.1;0.926258,MA0084.1;1.42483,MA0087.1;0.885691,MA0088.1;0.199853,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;0.239768,MA0117.1;0.956472,MA0119.1;2.47319,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;1.46857,MA0140.1;0.516266,MA0141.1;0.359385,MA0142.1;0.724856,MA0143.1;0.615094,MA0144.1;0.218541,MA0145.1;0.0613434,MA0146.1;0.00761723,MA0147.1;1.95811,MA0148.1;0.480298,MA0149.1;0.506665,MA0062.2;0.161302,MA0035.2;0.515566,MA0039.2;0.0325944,MA0138.2;0.653421,MA0002.2;0.179788,MA0137.2;0.321796,MA0104.2;1.05746,MA0047.2;0.586412,MA0112.2;0.0572179,MA0065.2;2.34319,MA0150.1;0.386144,MA0151.1;0,MA0152.1;0.52279,MA0153.1;1.01778,MA0154.1;0.577214,MA0155.1;4.06872,MA0156.1;0.323987,MA0157.1;0.697424,MA0158.1;0,MA0159.1;1.26616,MA0160.1;0.495355,MA0161.1;0,MA0162.1;0.378102,MA0163.1;0.0517199,MA0164.1;0.627336,MA0080.2;0.303167,MA0018.2;0.599912,MA0099.2;0.523145,MA0079.2;0.609448,MA0102.2;1.46209,MA0258.1;0.209744,MA0259.1;1.29349,MA0442.1;0
}}
}}

Revision as of 19:40, 22 January 2013


Full id: C1067_ductus_salivary_smooth_submaxillary_medial_parotid_seminal



Phase1 CAGE Peaks

Hg19::chr1:239549856..239549887,+p1@CHRM3
Hg19::chr1:239549889..239549900,+p5@CHRM3
Hg19::chr1:239549933..239549960,+p2@CHRM3
Hg19::chr1:239549963..239549974,+p6@CHRM3
Hg19::chr1:239550009..239550033,+p4@CHRM3
Hg19::chr1:239550209..239550229,+p8@CHRM3
Hg19::chr1:239550243..239550304,+p3@CHRM3
Hg19::chr1:239872062..239872067,+p@chr1:239872062..239872067
+


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><br>uberon_data<br><br>

Uber Anatomy
Ontology termp-valuen
adult organism7.71e-53114
central nervous system4.55e-4181
brain3.82e-3968
future brain3.82e-3968
nervous system6.15e-3889
neural tube4.11e-3756
neural rod4.11e-3756
future spinal cord4.11e-3756
neural keel4.11e-3756
regional part of nervous system3.05e-3653
regional part of brain3.05e-3653
regional part of forebrain4.36e-3541
forebrain4.36e-3541
anterior neural tube4.36e-3541
future forebrain4.36e-3541
cerebral hemisphere1.97e-3332
telencephalon5.57e-3334
brain grey matter9.77e-3334
gray matter9.77e-3334
regional part of cerebral cortex3.10e-3122
organ system subdivision4.61e-31223
regional part of telencephalon7.48e-3132
neocortex9.23e-2920
cerebral cortex1.36e-2625
pallium1.36e-2625
neural plate5.29e-2482
presumptive neural plate5.29e-2482
pre-chordal neural plate2.01e-2361
neurectoderm3.66e-2286
ectoderm-derived structure2.80e-18171
ectoderm2.80e-18171
presumptive ectoderm2.80e-18171
ecto-epithelium1.57e-17104
anatomical cluster1.19e-16373
structure with developmental contribution from neural crest8.64e-16132
multi-tissue structure7.80e-12342
organ2.75e-11503
temporal lobe1.89e-106
gyrus1.42e-096
multi-cellular organism2.99e-09656
embryo1.26e-08592
anatomical conduit1.51e-08240
basal ganglion2.15e-089
nuclear complex of neuraxis2.15e-089
aggregate regional part of brain2.15e-089
collection of basal ganglia2.15e-089
cerebral subcortex2.15e-089
occipital lobe3.25e-085
limbic system5.40e-085
parietal lobe7.75e-085
neural nucleus1.11e-079
nucleus of brain1.11e-079
anatomical system1.44e-07624
anatomical group1.68e-07625
brainstem3.29e-076
developing anatomical structure5.26e-07581
tube5.90e-07192
embryonic structure9.36e-07564


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)
MA0003.10.797136
MA0004.10.455723
MA0006.12.25059
MA0007.10.437331
MA0009.10.918715
MA0014.10.275152
MA0017.10.337901
MA0019.10.602411
MA0024.10.813542
MA0025.11.05265
MA0027.12.5321
MA0028.10.846854
MA0029.10.832916
MA0030.10.821423
MA0031.10.756713
MA0038.10.557409
MA0040.10.838784
MA0041.10.474018
MA0042.10.442535
MA0043.10.919032
MA0046.10.90778
MA0048.10.653157
MA0050.10.443405
MA0051.10.553205
MA0052.10.842664
MA0055.12.12623
MA0056.10
MA0057.10.305162
MA0058.10.362328
MA0059.10.361075
MA0060.10.190336
MA0061.10.165998
MA0063.10
MA0066.10.557833
MA0067.11.23721
MA0068.10.133123
MA0069.10.903908
MA0070.10.892666
MA0071.10.518907
MA0072.10.888148
MA0073.10.000871324
MA0074.10.552456
MA0076.10.377799
MA0077.10.880402
MA0078.10.652193
MA0081.12.54896
MA0083.10.926258
MA0084.11.42483
MA0087.10.885691
MA0088.10.199853
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
MA0116.10.239768
MA0117.10.956472
MA0119.12.47319
MA0122.10.982472
MA0124.11.11898
MA0125.11.0347
MA0130.10
MA0131.10.670358
MA0132.10
MA0133.10
MA0135.10.949204
MA0136.10.564434
MA0139.11.46857
MA0140.10.516266
MA0141.10.359385
MA0142.10.724856
MA0143.10.615094
MA0144.10.218541
MA0145.10.0613434
MA0146.10.00761723
MA0147.11.95811
MA0148.10.480298
MA0149.10.506665
MA0062.20.161302
MA0035.20.515566
MA0039.20.0325944
MA0138.20.653421
MA0002.20.179788
MA0137.20.321796
MA0104.21.05746
MA0047.20.586412
MA0112.20.0572179
MA0065.22.34319
MA0150.10.386144
MA0151.10
MA0152.10.52279
MA0153.11.01778
MA0154.10.577214
MA0155.14.06872
MA0156.10.323987
MA0157.10.697424
MA0158.10
MA0159.11.26616
MA0160.10.495355
MA0161.10
MA0162.10.378102
MA0163.10.0517199
MA0164.10.627336
MA0080.20.303167
MA0018.20.599912
MA0099.20.523145
MA0079.20.609448
MA0102.21.46209
MA0258.10.209744
MA0259.11.29349
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#1066474.690224326440655.26249365325459e-050.00089367410512562
HDAC2#306658.384762647891410.000106287309381870.00148105941354678
RAD21#588579.060654658524295.73112922357867e-072.63796123834876e-05
REST#597878.443775126612029.32603392806583e-073.99836476770635e-05
ZNF263#1012777.194111432384342.81251959700937e-069.71994487730183e-05



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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