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Coexpression cluster:C1726: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=0.508327,2.22212,0.500341,0.654974,0.454983,0.653236,0.733342,0.866061,0.321368,1.70183,2.55627,0.778743,0.274093,0.721271,0.453496,0.478935,0.963929,0.395009,0.287891,0.167776,0.500405,0.121147,1.55551,0.44943,0.549618,0.802434,0.25115,0.642741,10.416,0.659743,0.598009,1.00172,0.359091,0.27659,0.417272,0.432883,0.413782,0.654459,0.388123,0.301779,0.415749,0.580638,0.821929,0.451846,0.824538,0.533483,0.734485,3.67746,0.393318,0.458489,0.817229,1.76707,0.560115,1.08035,1.2359,0.724351,0.4631,0.689906,0.233662,1.64682,1.04369,0.736968,0.321912,2.15436,0.755773,0.899893,1.32544,1.69665,0.991065,1.53343,1.39076,2.40018,1.66643,1.23387,1.36104,0.709554,0.240727,0.917983,0.987729,0.543014,0.796279,0.934302,0.755403,0.327263,1.18161,0.0719601,0.166306,1.20877,0.844289,1.79645,1.41984,1.15413,1.01895,0.367039,4.06216,0.381528,0.28626,1.06255,0.849074,0.211081,0.389604,1.01316,1.05685,0.967698,0.88799,0.616433,0.951411,0.717647,0.549347,0.437618,0.512457,1.05402,0.494368,1.52665,1.37132,0.412056,1.49495,0.596731,0.897476,0.370186,1.22546,0.841768,0.650322,0.767198,1.48307,0.918767,1.72534,2.33502,1.2687,0.382577,2.60032,0.601055,1.28328,5.76396,1.43285,0.221105,0.591636,0.643339,1.38998,2.25246,1.84906,1.35224,0.728494,1.05895,0.889806,0.680988,0.87256,2.09294,0.577088,0.363423,0.526389,0.79475,1.15522,0.312599,0.736459,1.56426,0.827475,0.439798,0.54968,1.2893,1.35101,1.13636,5.27199,1.29666,0.906429,0.754576,0.35004,0.731946,0.0214572
|tfbs_overrepresentation_for_novel_motifs=0.508327,2.22212,0.500341,0.654974,0.454983,0.653236,0.733342,0.866061,0.321368,1.70183,2.55627,0.778743,0.274093,0.721271,0.453496,0.478935,0.963929,0.395009,0.287891,0.167776,0.500405,0.121147,1.55551,0.44943,0.549618,0.802434,0.25115,0.642741,10.416,0.659743,0.598009,1.00172,0.359091,0.27659,0.417272,0.432883,0.413782,0.654459,0.388123,0.301779,0.415749,0.580638,0.821929,0.451846,0.824538,0.533483,0.734485,3.67746,0.393318,0.458489,0.817229,1.76707,0.560115,1.08035,1.2359,0.724351,0.4631,0.689906,0.233662,1.64682,1.04369,0.736968,0.321912,2.15436,0.755773,0.899893,1.32544,1.69665,0.991065,1.53343,1.39076,2.40018,1.66643,1.23387,1.36104,0.709554,0.240727,0.917983,0.987729,0.543014,0.796279,0.934302,0.755403,0.327263,1.18161,0.0719601,0.166306,1.20877,0.844289,1.79645,1.41984,1.15413,1.01895,0.367039,4.06216,0.381528,0.28626,1.06255,0.849074,0.211081,0.389604,1.01316,1.05685,0.967698,0.88799,0.616433,0.951411,0.717647,0.549347,0.437618,0.512457,1.05402,0.494368,1.52665,1.37132,0.412056,1.49495,0.596731,0.897476,0.370186,1.22546,0.841768,0.650322,0.767198,1.48307,0.918767,1.72534,2.33502,1.2687,0.382577,2.60032,0.601055,1.28328,5.76396,1.43285,0.221105,0.591636,0.643339,1.38998,2.25246,1.84906,1.35224,0.728494,1.05895,0.889806,0.680988,0.87256,2.09294,0.577088,0.363423,0.526389,0.79475,1.15522,0.312599,0.736459,1.56426,0.827475,0.439798,0.54968,1.2893,1.35101,1.13636,5.27199,1.29666,0.906429,0.754576,0.35004,0.731946,0.0214572
|tfbs_overrepresentation_jaspar=MA0003.1;0.136928,MA0004.1;0.626788,MA0006.1;0.452993,MA0007.1;0.606704,MA0009.1;1.11255,MA0014.1;0.0418333,MA0017.1;0.496101,MA0019.1;0.784036,MA0024.1;1.00439,MA0025.1;1.24931,MA0027.1;2.73598,MA0028.1;0.470679,MA0029.1;1.02437,MA0030.1;1.01252,MA0031.1;0.945567,MA0038.1;1.7452,MA0040.1;1.03042,MA0041.1;0.64667,MA0042.1;0.612397,MA0043.1;1.11288,MA0046.1;1.10134,MA0048.1;0.195817,MA0050.1;0.613347,MA0051.1;0.731787,MA0052.1;1.03442,MA0055.1;0.0853006,MA0056.1;0,MA0057.1;1.05691,MA0058.1;0.523638,MA0059.1;1.29682,MA0060.1;4.22932,MA0061.1;0.291022,MA0063.1;0,MA0066.1;2.92423,MA0067.1;1.43651,MA0068.1;0.247962,MA0069.1;1.09737,MA0070.1;1.08584,MA0071.1;0.695094,MA0072.1;1.0812,MA0073.1;2.08296,MA0074.1;0.730989,MA0076.1;0.540943,MA0077.1;1.07324,MA0078.1;0.836493,MA0081.1;0.522409,MA0083.1;1.12028,MA0084.1;1.62584,MA0087.1;1.07867,MA0088.1;0.132006,MA0089.1;0,MA0090.1;0.556637,MA0091.1;0.629594,MA0092.1;0.588959,MA0093.1;0.456342,MA0095.1;0,MA0098.1;0,MA0100.1;2.96921,MA0101.1;0.459973,MA0103.1;0.442769,MA0105.1;1.00065,MA0106.1;0.779931,MA0107.1;0.985964,MA0108.2;0.94238,MA0109.1;0,MA0111.1;1.40074,MA0113.1;0.797251,MA0114.1;0.372523,MA0115.1;1.35895,MA0116.1;0.382106,MA0117.1;1.1512,MA0119.1;0.504689,MA0122.1;1.17777,MA0124.1;1.31673,MA0125.1;1.23103,MA0130.1;0,MA0131.1;0.855546,MA0132.1;0,MA0133.1;0,MA0135.1;1.14377,MA0136.1;0.743749,MA0139.1;1.39016,MA0140.1;0.692258,MA0141.1;0.520334,MA0142.1;0.912455,MA0143.1;0.797437,MA0144.1;0.356507,MA0145.1;0.143698,MA0146.1;0.0359558,MA0147.1;0.386018,MA0148.1;0.653474,MA0149.1;0.681935,MA0062.2;0.284987,MA0035.2;0.691506,MA0039.2;0.801354,MA0138.2;0.837782,MA0002.2;0.30855,MA0137.2;0.47779,MA0104.2;0.320919,MA0047.2;0.767096,MA0112.2;0.136971,MA0065.2;0.449243,MA0150.1;0.550239,MA0151.1;0,MA0152.1;0.69926,MA0153.1;1.21379,MA0154.1;0.172764,MA0155.1;0.130813,MA0156.1;0.480289,MA0157.1;0.883854,MA0158.1;0,MA0159.1;0.386729,MA0160.1;0.669748,MA0161.1;0,MA0162.1;0.469165,MA0163.1;0.0439995,MA0164.1;3.15573,MA0080.2;0.456437,MA0018.2;0.781393,MA0099.2;0.699641,MA0079.2;1.81596,MA0102.2;1.66336,MA0258.1;0.345771,MA0259.1;1.02361,MA0442.1;0
}}
}}

Revision as of 20:08, 22 January 2013


Full id: C1726_acute_Lens_pituitary_Ciliary_eye_H9_retina



Phase1 CAGE Peaks

Hg19::chr14:60975644..60975673,+p3@SIX6
Hg19::chr14:60975858..60975869,+p2@SIX6
Hg19::chr14:60975871..60975880,+p4@SIX6
Hg19::chr14:60975883..60975911,+p1@SIX6
Hg19::chr14:60975914..60975925,+p5@SIX6


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>

Uber Anatomy
Ontology termp-valuen
pigment epithelium of eye2.55e-3111
atypical epithelium3.50e-294
eye3.08e-2621
visual system3.08e-2621
anterior segment of eyeball1.93e-2414
sense organ8.79e-2324
sensory system8.79e-2324
entire sense organ system8.79e-2324
ciliary epithelium1.61e-223
ciliary body1.61e-223
camera-type eye7.09e-2220
simple eye7.09e-2220
immature eye7.09e-2220
ocular region7.09e-2220
eyeball of camera-type eye7.09e-2220
optic cup7.09e-2220
optic vesicle7.09e-2220
eye primordium7.09e-2220
face8.74e-2022
vasculature of eye1.54e-196
uvea1.54e-196
vasculature of head1.54e-196
cuboidal epithelium7.88e-174
transparent eye structure7.88e-174
simple cuboidal epithelium7.88e-174
cranial placode7.88e-174
lens of camera-type eye7.88e-174
epithelium of lens7.88e-174
lens placode7.88e-174
lens vesicle7.88e-174
vasculature of organ4.43e-1611
pituitary gland1.65e-152
ectodermal placode1.04e-1331
pre-chordal neural plate7.04e-1061
external ectoderm1.16e-088
iris epithelium2.02e-081
iris2.02e-081
ectoderm-derived structure2.75e-08171
ectoderm2.75e-08171
presumptive ectoderm2.75e-08171
subdivision of head3.02e-0849
gland of diencephalon3.45e-084
neuroendocrine gland3.45e-084
dura mater6.24e-081
future meninx6.24e-081
ectomeninx6.24e-081
future dura mater6.24e-081
head4.51e-0756
neural plate5.98e-0782
presumptive neural plate5.98e-0782


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)
MA0003.10.136928
MA0004.10.626788
MA0006.10.452993
MA0007.10.606704
MA0009.11.11255
MA0014.10.0418333
MA0017.10.496101
MA0019.10.784036
MA0024.11.00439
MA0025.11.24931
MA0027.12.73598
MA0028.10.470679
MA0029.11.02437
MA0030.11.01252
MA0031.10.945567
MA0038.11.7452
MA0040.11.03042
MA0041.10.64667
MA0042.10.612397
MA0043.11.11288
MA0046.11.10134
MA0048.10.195817
MA0050.10.613347
MA0051.10.731787
MA0052.11.03442
MA0055.10.0853006
MA0056.10
MA0057.11.05691
MA0058.10.523638
MA0059.11.29682
MA0060.14.22932
MA0061.10.291022
MA0063.10
MA0066.12.92423
MA0067.11.43651
MA0068.10.247962
MA0069.11.09737
MA0070.11.08584
MA0071.10.695094
MA0072.11.0812
MA0073.12.08296
MA0074.10.730989
MA0076.10.540943
MA0077.11.07324
MA0078.10.836493
MA0081.10.522409
MA0083.11.12028
MA0084.11.62584
MA0087.11.07867
MA0088.10.132006
MA0089.10
MA0090.10.556637
MA0091.10.629594
MA0092.10.588959
MA0093.10.456342
MA0095.10
MA0098.10
MA0100.12.96921
MA0101.10.459973
MA0103.10.442769
MA0105.11.00065
MA0106.10.779931
MA0107.10.985964
MA0108.20.94238
MA0109.10
MA0111.11.40074
MA0113.10.797251
MA0114.10.372523
MA0115.11.35895
MA0116.10.382106
MA0117.11.1512
MA0119.10.504689
MA0122.11.17777
MA0124.11.31673
MA0125.11.23103
MA0130.10
MA0131.10.855546
MA0132.10
MA0133.10
MA0135.11.14377
MA0136.10.743749
MA0139.11.39016
MA0140.10.692258
MA0141.10.520334
MA0142.10.912455
MA0143.10.797437
MA0144.10.356507
MA0145.10.143698
MA0146.10.0359558
MA0147.10.386018
MA0148.10.653474
MA0149.10.681935
MA0062.20.284987
MA0035.20.691506
MA0039.20.801354
MA0138.20.837782
MA0002.20.30855
MA0137.20.47779
MA0104.20.320919
MA0047.20.767096
MA0112.20.136971
MA0065.20.449243
MA0150.10.550239
MA0151.10
MA0152.10.69926
MA0153.11.21379
MA0154.10.172764
MA0155.10.130813
MA0156.10.480289
MA0157.10.883854
MA0158.10
MA0159.10.386729
MA0160.10.669748
MA0161.10
MA0162.10.469165
MA0163.10.0439995
MA0164.13.15573
MA0080.20.456437
MA0018.20.781393
MA0099.20.699641
MA0079.21.81596
MA0102.21.66336
MA0258.10.345771
MA0259.11.02361
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
CTBP2#1488562.71700033932811.02712351233917e-099.50990713698493e-08
CTCF#1066444.288205098460020.005152015588243280.0239323647209242
REST#597859.650028716128021.19441074361324e-050.000301457379536546
SIN3A#2594255.408884726815140.0002159522671657270.00247926116637588
SUZ12#23512550.11578091106293.15480790456198e-092.61911750989308e-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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