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Coexpression cluster:C1916: Difference between revisions

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{{Coexpression_clusters
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3,0.00149378,0.0538978,0.0537285,0.15063,0.198077,0.281455,0.348739,0.419895,0.138495,0.208834,0.32256,0.377566,0.342366,0.109684,0.0587975,0.403482,0.181288,0.0289693,0.352328,0.255358,0.351665,0.265112,4.44445e-05,0.10772,0.0854747,0.0747609,0.406458,0.312881,0.162482,0.244656,0.192188,0.158985,0.00101224,0.0972854,0.333309,0.249919,0.339517,0.303699,0.198326,0.394084,0.458518,0.282501,0.252005,0.390891,0.238377,0.334983,0.197875,0.287909,0.289389,0.117618,0.392533,0.396962,0.316002,0.330317,0.00728437,0.0274786,0.300542,0.379651,0.185715,0.345505,0.0814929,0.271405,0.311201,0.221943,0.306427,0.367733,0.246925,0.208775,0.390438,0.343014,0.270094,0.276922,0.156279,0.0067183,0.461742,0.422872,0.336468,0.000438215,0.313545,0.17149,0.0877361,0.0880065,0.238969,0.126615,0.0669467,0.0879453,0.474066,0.396935,0.326779,0.292869,0.358198,0.29552,0.131776,0.158116,0.104606,0.194814,0.104167,0.168186,0.108081,0.123829,0.205215,0.175247,6.69639e-05,0.109077,0.144842,0.0604892,0.214671,0.316879,0.442567,0.430541,0.159424,0.224871,0.0150771,0.389061,0.310732,0.349611,0.445995,0.385709,0.278202,0.426488,0.400591,0.209809,0.0351523,0.319519,0.309489,0.430805,0.362154,0.480785,0.185476,0.336314,0.344469,0.184651,0.303359,0.297596,0.42392,0.425912,0.380826,0.259046,0.345068,0.151046,0.483953,0.347171,0.321735,0.0126239,0.13907,0.470121,0.269432,0.250466,0.409882,0.115686,0.408975,0.162633,0.342661,0.27567,0.248127,0.33299,0.384731,0.319112,0.526476|tfbs_overrepresentation_for_novel_motifs=0.508327,1.20042,2.1621,0.654974,0.454983,0.653236,1.73914,0.324142,1.55025,2.31449,0.621241,0.778743,0.752887,0.721271,0.453496,0.478935,0.963929,0.395009,0.287891,2.20431,0.500405,0.770467,0.645033,0.44943,2.3241,0.802434,0.700122,0.642741,1.16016,1.22891,0.598009,1.00172,0.359091,0.27659,0.417272,0.757784,0.413782,0.654459,0.388123,0.815792,0.415749,0.580638,0.821929,0.451846,1.74542,0.533483,0.734485,1.48156,0.124583,2.02272,0.817229,0.746838,0.560115,1.08035,1.2359,0.724351,0.4631,0.689906,0.659455,1.64682,1.04369,0.736968,0.86107,0.935408,0.755773,0.899893,1.32544,1.69665,0.991065,1.53343,0.566575,0.330474,1.66643,1.23387,2.09345,0.255232,0.675933,2.11876,0.987729,0.543014,0.293154,3.54148,0.755403,0.327263,1.18161,0.0719601,0.166306,0.228496,0.844289,1.79645,1.41984,1.15413,1.01895,0.367039,0.455791,0.381528,0.28626,1.06255,0.849074,0.606298,0.389604,1.01316,1.05685,0.967698,0.88799,0.616433,0.951411,0.717647,0.549347,2.90764,1.27602,1.05402,1.23742,0.631235,1.37132,1.05995,1.00558,0.596731,0.897476,0.370186,1.22546,0.841768,0.650322,0.767198,1.48307,2.12036,1.72534,1.02407,1.2687,0.995523,1.15483,0.601055,1.28328,0.763715,1.43285,0.221105,0.591636,0.643339,1.38998,2.25246,1.84906,1.35224,0.728494,2.4059,2.06113,0.680988,0.87256,2.09294,0.577088,2.55945,0.177807,1.87689,1.15522,0.840171,0.736459,1.56426,0.827475,0.439798,0.54968,0.518696,1.35101,1.13636,0.98692,0.522159,0.906429,0.754576,1.65153,0.731946,0.0938701|tfbs_overrepresentation_jaspar=MA0003.1;1.80249,MA0004.1;0.626788,MA0006.1;1.14863,MA0007.1;0.606704,MA0009.1;1.11255,MA0014.1;3.71305,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;0.736268,MA0040.1;1.03042,MA0041.1;0.64667,MA0042.1;0.612397,MA0043.1;1.11288,MA0046.1;1.10134,MA0048.1;0.569896,MA0050.1;0.613347,MA0051.1;1.73592,MA0052.1;1.03442,MA0055.1;0.288856,MA0056.1;0,MA0057.1;0.189508,MA0058.1;0.523638,MA0059.1;3.2914,MA0060.1;1.55172,MA0061.1;0.291022,MA0063.1;0,MA0066.1;0.736721,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;0.215829,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;1.3271,MA0089.1;0,MA0090.1;2.34702,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;1.12656,MA0105.1;0.175503,MA0106.1;0.779931,MA0107.1;0.378225,MA0108.2;0.94238,MA0109.1;0,MA0111.1;0.5713,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;1.99092,MA0132.1;0,MA0133.1;0,MA0135.1;1.14377,MA0136.1;0.743749,MA0139.1;0.277033,MA0140.1;4.03435,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;2.66688,MA0148.1;0.653474,MA0149.1;0.681935,MA0062.2;0.777733,MA0035.2;2.78095,MA0039.2;0.311551,MA0138.2;0.837782,MA0002.2;0.83106,MA0137.2;0.47779,MA0104.2;3.24989,MA0047.2;0.767096,MA0112.2;0.136971,MA0065.2;1.41695,MA0150.1;0.550239,MA0151.1;0,MA0152.1;0.69926,MA0153.1;1.21379,MA0154.1;1.57192,MA0155.1;0.813062,MA0156.1;0.480289,MA0157.1;0.883854,MA0158.1;0,MA0159.1;2.67024,MA0160.1;0.669748,MA0161.1;0,MA0162.1;1.72541,MA0163.1;0.0439995,MA0164.1;0.810347,MA0080.2;1.15604,MA0018.2;0.781393,MA0099.2;1.66926,MA0079.2;1.53298,MA0102.2;1.66336,MA0258.1;1.63655,MA0259.1;0.395396,MA0442.1;0}}
|full_id=C1916_Fibroblast_amniotic_Adipocyte_Smooth_immature_CD14_normal
|id=C1916
}}

Latest revision as of 11:54, 17 September 2013


Full id: C1916_Fibroblast_amniotic_Adipocyte_Smooth_immature_CD14_normal



Phase1 CAGE Peaks

Hg19::chr3:105085383..105085403,+p7@ALCAM
Hg19::chr3:105085428..105085442,+p6@ALCAM
Hg19::chr3:105085548..105085584,+p2@ALCAM
Hg19::chr3:105085587..105085610,+p3@ALCAM
Hg19::chr3:105085734..105085760,+p1@ALCAM


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
fibroblast1.29e-0976
Uber Anatomy
Ontology termp-valuen
multi-cellular organism3.68e-11656
embryonic structure2.08e-10564
anatomical system2.16e-10624
developing anatomical structure2.68e-10581
anatomical group4.08e-10625
germ layer4.17e-10560
germ layer / neural crest4.17e-10560
embryonic tissue4.17e-10560
presumptive structure4.17e-10560
germ layer / neural crest derived structure4.17e-10560
epiblast (generic)4.17e-10560
embryo2.08e-08592
musculoskeletal system2.12e-08167
neural tube2.47e-0856
neural rod2.47e-0856
future spinal cord2.47e-0856
neural keel2.47e-0856
neural plate2.57e-0882
presumptive neural plate2.57e-0882
structure with developmental contribution from neural crest4.44e-08132
organ1.29e-07503
regional part of nervous system1.30e-0753
regional part of brain1.30e-0753
ectoderm-derived structure1.33e-07171
ectoderm1.33e-07171
presumptive ectoderm1.33e-07171
neurectoderm1.47e-0786
brain2.36e-0768
future brain2.36e-0768
skeletal system5.80e-07100
pre-chordal neural plate6.59e-0761
regional part of forebrain8.10e-0741
forebrain8.10e-0741
anterior neural tube8.10e-0741
future forebrain8.10e-0741


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)
MA0003.11.80249
MA0004.10.626788
MA0006.11.14863
MA0007.10.606704
MA0009.11.11255
MA0014.13.71305
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
MA0038.10.736268
MA0040.11.03042
MA0041.10.64667
MA0042.10.612397
MA0043.11.11288
MA0046.11.10134
MA0048.10.569896
MA0050.10.613347
MA0051.11.73592
MA0052.11.03442
MA0055.10.288856
MA0056.10
MA0057.10.189508
MA0058.10.523638
MA0059.13.2914
MA0060.11.55172
MA0061.10.291022
MA0063.10
MA0066.10.736721
MA0067.11.43651
MA0068.10.247962
MA0069.11.09737
MA0070.11.08584
MA0071.10.695094
MA0072.11.0812
MA0073.10.215829
MA0074.10.730989
MA0076.10.540943
MA0077.11.07324
MA0078.10.836493
MA0081.10.522409
MA0083.11.12028
MA0084.11.62584
MA0087.11.07867
MA0088.11.3271
MA0089.10
MA0090.12.34702
MA0091.10.629594
MA0092.10.588959
MA0093.10.456342
MA0095.10
MA0098.10
MA0100.12.96921
MA0101.10.459973
MA0103.11.12656
MA0105.10.175503
MA0106.10.779931
MA0107.10.378225
MA0108.20.94238
MA0109.10
MA0111.10.5713
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
MA0131.11.99092
MA0132.10
MA0133.10
MA0135.11.14377
MA0136.10.743749
MA0139.10.277033
MA0140.14.03435
MA0141.10.520334
MA0142.10.912455
MA0143.10.797437
MA0144.10.356507
MA0145.10.143698
MA0146.10.0359558
MA0147.12.66688
MA0148.10.653474
MA0149.10.681935
MA0062.20.777733
MA0035.22.78095
MA0039.20.311551
MA0138.20.837782
MA0002.20.83106
MA0137.20.47779
MA0104.23.24989
MA0047.20.767096
MA0112.20.136971
MA0065.21.41695
MA0150.10.550239
MA0151.10
MA0152.10.69926
MA0153.11.21379
MA0154.11.57192
MA0155.10.813062
MA0156.10.480289
MA0157.10.883854
MA0158.10
MA0159.12.67024
MA0160.10.669748
MA0161.10
MA0162.11.72541
MA0163.10.0439995
MA0164.10.810347
MA0080.21.15604
MA0018.20.781393
MA0099.21.66926
MA0079.21.53298
MA0102.21.66336
MA0258.11.63655
MA0259.10.395396
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#1066455.360256373075030.0002259278299937090.00250060159354736
E2F1#186954.907389214879320.0003512818099256460.00353308175527971
E2F4#1874512.66806031528443.06319883889696e-060.00010356666349484
E2F6#187655.017155731697390.0003144978599297790.00323095042231027
ELF1#199754.258097958807540.0007142416939776840.00573584684946831
FOS#235358.99795530889441.69470025615156e-050.000389594541167098
GATA2#2624512.7449317335542.9719152914525e-060.000101234136048274
JUND#372745.595731153496820.001849593301755460.0109376408381201
MAX#414956.452555509007128.93743970843928e-050.00130749021671059
MYC#460955.22228187160940.0002573944848850610.00276706357250755
NFKB1#479055.488063424193840.0002008162847462320.00239254528434995
NR3C1#2908411.97841866493849.4122920812787e-050.00136643087667037
PAX5#507945.335652424942260.002223389586187790.0127811858758183
RAD21#5885510.35503389545638.39503550283973e-060.000229701103715242
SMC3#9126515.04493284493281.29633924985553e-065.16355358183302e-05
SP1#666755.69838137814090.000166391843712550.00204444679594059
TAF1#687253.343046285745290.002394600090870310.0135483850095024
TCF12#693836.380678941311850.007185168653258840.0298350758976503
USF1#739156.361499277207969.59569864925045e-050.00137020121852484
YY1#752854.911170749853860.00034993140821360.00352901567617035
ZNF143#7702410.80070124178230.0001415223430863190.00184455909017747



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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