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{{Coexpression_clusters
{
|full_id=C139_astrocytoma_skin_salivary_gall_serous_Mallassezderived_renal
|

Latest revision as of 10:40, 17 September 2013


Full id: C139_astrocytoma_skin_salivary_gall_serous_Mallassezderived_renal



Phase1 CAGE Peaks

Hg19::chr10:105846063..105846083,-p5@COL17A1
Hg19::chr11:107418886..107418917,+p@chr11:107418886..107418917
+
Hg19::chr11:117152313..117152356,+p4@RNF214
Hg19::chr11:117152405..117152414,+p17@RNF214
Hg19::chr11:117152437..117152448,+p12@RNF214
Hg19::chr11:117152450..117152451,+p21@RNF214
Hg19::chr11:20057481..20057496,+p@chr11:20057481..20057496
+
Hg19::chr11:5064816..5064825,+p@chr11:5064816..5064825
+
Hg19::chr11:86334270..86334280,+p@chr11:86334270..86334280
+
Hg19::chr11:9754117..9754125,+p13@SWAP70
Hg19::chr12:132475501..132475504,+p@chr12:132475501..132475504
+
Hg19::chr12:132475623..132475637,+p@chr12:132475623..132475637
+
Hg19::chr12:41374693..41374709,+p@chr12:41374693..41374709
+
Hg19::chr12:41374715..41374720,+p@chr12:41374715..41374720
+
Hg19::chr12:41374726..41374748,+p@chr12:41374726..41374748
+
Hg19::chr12:41374749..41374779,+p@chr12:41374749..41374779
+
Hg19::chr12:41374792..41374806,+p@chr12:41374792..41374806
+
Hg19::chr12:41374821..41374828,+p@chr12:41374821..41374828
+
Hg19::chr12:41374830..41374843,+p@chr12:41374830..41374843
+
Hg19::chr13:45781332..45781345,+p@chr13:45781332..45781345
+
Hg19::chr13:94958313..94958338,+p@chr13:94958313..94958338
+
Hg19::chr14:36998889..36998925,+p@chr14:36998889..36998925
+
Hg19::chr14:56711322..56711331,+p@chr14:56711322..56711331
+
Hg19::chr15:36653779..36653789,-p@chr15:36653779..36653789
-
Hg19::chr15:40069726..40069746,-p@chr15:40069726..40069746
-
Hg19::chr15:49217959..49217969,-p@chr15:49217959..49217969
-
Hg19::chr15:49217985..49217990,-p@chr15:49217985..49217990
-
Hg19::chr15:49255230..49255248,-p16@SHC4
Hg19::chr15:49255569..49255578,-p20@SHC4
Hg19::chr15:99434469..99434480,+p@chr15:99434469..99434480
+
Hg19::chr15:99434544..99434559,+p@chr15:99434544..99434559
+
Hg19::chr15:99434663..99434673,+p@chr15:99434663..99434673
+
Hg19::chr16:85617034..85617043,-p@chr16:85617034..85617043
-
Hg19::chr16:85617044..85617059,-p@chr16:85617044..85617059
-
Hg19::chr16:85617064..85617073,-p@chr16:85617064..85617073
-
Hg19::chr16:85617082..85617098,-p@chr16:85617082..85617098
-
Hg19::chr16:85617170..85617191,-p@chr16:85617170..85617191
-
Hg19::chr16:85617192..85617217,-p@chr16:85617192..85617217
-
Hg19::chr17:15555123..15555141,-p4@TRIM16
Hg19::chr17:6099834..6099873,+p@chr17:6099834..6099873
+
Hg19::chr18:11391769..11391782,-p@chr18:11391769..11391782
-
Hg19::chr18:55721963..55721974,+p40@NEDD4L
Hg19::chr18:55721981..55721992,+p42@NEDD4L
Hg19::chr18:63802163..63802169,+p@chr18:63802163..63802169
+
Hg19::chr18:63802179..63802185,+p@chr18:63802179..63802185
+
Hg19::chr18:63802190..63802197,+p@chr18:63802190..63802197
+
Hg19::chr18:66485720..66485728,+p@chr18:66485720..66485728
+
Hg19::chr18:66485736..66485758,+p@chr18:66485736..66485758
+
Hg19::chr18:9100027..9100043,+p@chr18:9100027..9100043
+
Hg19::chr18:9100055..9100067,+p@chr18:9100055..9100067
+
Hg19::chr1:109400845..109400854,-p5@AKNAD1
Hg19::chr1:109400860..109400871,-p3@AKNAD1
Hg19::chr1:152286943..152286949,+p@chr1:152286943..152286949
+
Hg19::chr1:152297708..152297722,-p1@FLG
Hg19::chr1:186946611..186946622,+p@chr1:186946611..186946622
+
Hg19::chr1:20608774..20608813,+p@chr1:20608774..20608813
+
Hg19::chr1:20609126..20609137,+p@chr1:20609126..20609137
+
Hg19::chr1:20609280..20609293,+p@chr1:20609280..20609293
+
Hg19::chr1:225962665..225962674,+p@chr1:225962665..225962674
+
Hg19::chr1:230921649..230921659,+p@chr1:230921649..230921659
+
Hg19::chr1:236072503..236072522,+p@chr1:236072503..236072522
+
Hg19::chr1:236072592..236072599,+p@chr1:236072592..236072599
+
Hg19::chr1:41898930..41898936,+p@chr1:41898930..41898936
+
Hg19::chr1:43310323..43310328,-p@chr1:43310323..43310328
-
Hg19::chr1:44872537..44872548,+p@chr1:44872537..44872548
+
Hg19::chr1:98552894..98552910,+p@chr1:98552894..98552910
+
Hg19::chr20:49983328..49983340,+p@chr20:49983328..49983340
+
Hg19::chr20:49983349..49983354,+p@chr20:49983349..49983354
+
Hg19::chr20:49983362..49983378,+p@chr20:49983362..49983378
+
Hg19::chr20:49983397..49983415,+p@chr20:49983397..49983415
+
Hg19::chr20:49983423..49983431,+p@chr20:49983423..49983431
+
Hg19::chr2:138989393..138989399,+p@chr2:138989393..138989399
+
Hg19::chr2:138989408..138989420,+p@chr2:138989408..138989420
+
Hg19::chr2:18479019..18479024,+p@chr2:18479019..18479024
+
Hg19::chr2:18479033..18479051,+p@chr2:18479033..18479051
+
Hg19::chr2:18479067..18479081,+p@chr2:18479067..18479081
+
Hg19::chr2:18479137..18479145,+p@chr2:18479137..18479145
+
Hg19::chr2:43364784..43364799,-p@chr2:43364784..43364799
-
Hg19::chr2:43364874..43364891,-p@chr2:43364874..43364891
-
Hg19::chr2:74069495..74069505,+p@chr2:74069495..74069505
+
Hg19::chr3:170807661..170807666,+p@chr3:170807661..170807666
+
Hg19::chr3:197205979..197205991,+p@chr3:197205979..197205991
+
Hg19::chr3:197206040..197206047,+p@chr3:197206040..197206047
+
Hg19::chr3:197206051..197206063,+p@chr3:197206051..197206063
+
Hg19::chr4:100981084..100981089,-p@chr4:100981084..100981089
-
Hg19::chr4:101018344..101018348,-p@chr4:101018344..101018348
-
Hg19::chr4:173473985..173473989,-p@chr4:173473985..173473989
-
Hg19::chr4:180386691..180386698,-p3@ENST00000512036
Hg19::chr4:186854216..186854237,-p23@SORBS2
Hg19::chr4:186854245..186854259,-p51@SORBS2
Hg19::chr4:186854275..186854287,-p39@SORBS2
Hg19::chr4:186854301..186854319,-p44@SORBS2
Hg19::chr4:186854336..186854358,-p41@SORBS2
Hg19::chr4:28429463..28429485,+p@chr4:28429463..28429485
+
Hg19::chr4:28429607..28429619,+p@chr4:28429607..28429619
+
Hg19::chr4:28429620..28429623,+p@chr4:28429620..28429623
+
Hg19::chr4:28609492..28609496,+p@chr4:28609492..28609496
+
Hg19::chr4:85791597..85791604,-p@chr4:85791597..85791604
-
Hg19::chr5:135331152..135331163,+p@chr5:135331152..135331163
+
Hg19::chr5:135540733..135540788,-p@chr5:135540733..135540788
-
Hg19::chr5:135540818..135540823,-p@chr5:135540818..135540823
-
Hg19::chr5:168213193..168213198,-p@chr5:168213193..168213198
-
Hg19::chr5:168213223..168213231,-p@chr5:168213223..168213231
-
Hg19::chr5:168213234..168213245,-p@chr5:168213234..168213245
-
Hg19::chr5:72708801..72708804,+p@chr5:72708801..72708804
+
Hg19::chr5:72708814..72708824,+p@chr5:72708814..72708824
+
Hg19::chr5:74964235..74964256,+p@chr5:74964235..74964256
+
Hg19::chr5:79140618..79140625,+p@chr5:79140618..79140625
+
Hg19::chr5:79140655..79140663,+p@chr5:79140655..79140663
+
Hg19::chr6:132527234..132527248,+p@chr6:132527234..132527248
+
Hg19::chr6:33749053..33749070,-p2@LEMD2
Hg19::chr6:33749073..33749084,-p6@LEMD2
Hg19::chr6:33749091..33749103,-p4@LEMD2
Hg19::chr7:3284005..3284016,-p@chr7:3284005..3284016
-
Hg19::chr7:3284027..3284034,-p@chr7:3284027..3284034
-
Hg19::chr7:48080786..48080793,+p@chr7:48080786..48080793
+
Hg19::chr7:48080805..48080813,+p@chr7:48080805..48080813
+
Hg19::chr7:48080821..48080824,+p@chr7:48080821..48080824
+
Hg19::chr7:48080850..48080853,+p@chr7:48080850..48080853
+
Hg19::chr7:48080858..48080881,+p@chr7:48080858..48080881
+
Hg19::chr7:48080895..48080908,+p@chr7:48080895..48080908
+
Hg19::chr7:48080923..48080931,+p@chr7:48080923..48080931
+
Hg19::chr7:48082461..48082477,+p@chr7:48082461..48082477
+
Hg19::chr9:137617930..137617940,+p@chr9:137617930..137617940
+
Hg19::chrX:134405649..134405699,+p@chrX:134405649..134405699
+
Hg19::chrX:134405722..134405726,+p@chrX:134405722..134405726
+
Hg19::chrX:139585644..139585652,-p@chrX:139585644..139585652
-
Hg19::chrX:139587228..139587234,-p1@SOX3


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:0055078sodium ion homeostasis0.0497417642587206
GO:0017080sodium channel regulator activity0.0497417642587206
GO:0006883cellular sodium ion homeostasis0.0497417642587206
GO:0030104water homeostasis0.0497417642587206
GO:0018987osmoregulation0.0497417642587206
GO:0032501multicellular organismal process0.0497417642587206
GO:0007275multicellular organismal development0.0497417642587206
GO:0002208somatic diversification of immunoglobulins during immune response0.0497417642587206
GO:0002381immunoglobulin production during immune response0.0497417642587206
GO:0002204somatic recombination of immunoglobulin genes during immune response0.0497417642587206
GO:0045190isotype switching0.0497417642587206
GO:0016447somatic recombination of immunoglobulin gene segments0.0497417642587206
GO:0030004cellular monovalent inorganic cation homeostasis0.0497417642587206
GO:0016444somatic cell DNA recombination0.0497417642587206
GO:0055067monovalent inorganic cation homeostasis0.0497417642587206
GO:0016445somatic diversification of immunoglobulins0.0497417642587206
GO:0002562somatic diversification of immune receptors via germline recombination within a single locus0.0497417642587206
GO:0002200somatic diversification of immune receptors0.0497417642587206
GO:0042176regulation of protein catabolic process0.0497417642587206
GO:0005637nuclear inner membrane0.0497417642587206
GO:0045807positive regulation of endocytosis0.0497417642587206
GO:0002377immunoglobulin production0.0497417642587206



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><br>disease_data<br>

Disease
Ontology termp-valuen
nervous system cancer6.76e-1811


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
MA0004.10.0396783
MA0006.10.0332698
MA0007.10.00249845
MA0009.10.0594703
MA0014.12.89298e-16
MA0017.10.0143326
MA0019.10.0771638
MA0024.10.127497
MA0025.10.111659
MA0027.11.33752
MA0028.10.000128804
MA0029.10.5994
MA0030.11.29877
MA0031.10.225871
MA0038.10.118739
MA0040.10.339513
MA0041.11.45121
MA0042.11.81478
MA0043.10.215739
MA0046.10.451488
MA0048.15.12637e-05
MA0050.11.22001
MA0051.11.06698
MA0052.10.62259
MA0055.10.00277025
MA0056.10
MA0057.13.01226e-06
MA0058.10.0228755
MA0059.10.0935014
MA0060.10.00307258
MA0061.10.00555983
MA0063.10
MA0066.10.0153071
MA0067.10.211111
MA0068.10.0454699
MA0069.12.1975
MA0070.12.71338
MA0071.10.886264
MA0072.11.12892
MA0073.18.32659e-09
MA0074.10.00225856
MA0076.17.3246e-05
MA0077.11.10186
MA0078.10.94305
MA0081.10.159546
MA0083.10.0619278
MA0084.10.898735
MA0087.11.57881
MA0088.10.000373771
MA0089.10
MA0090.10.139966
MA0091.11.63536
MA0092.10.827044
MA0093.10.00654264
MA0095.10
MA0098.10
MA0100.10.0179189
MA0101.10.119714
MA0103.10.0536062
MA0105.19.11806e-07
MA0106.10.00418723
MA0107.10.000226393
MA0108.20.424746
MA0109.10
MA0111.10.0922393
MA0113.10.0859225
MA0114.10.00221079
MA0115.10.16627
MA0116.10.2963
MA0117.10.538585
MA0119.10.586286
MA0122.13.31496
MA0124.10.442689
MA0125.10.338455
MA0130.10
MA0131.10.00938838
MA0132.10
MA0133.10
MA0135.10.245279
MA0136.10.126221
MA0139.13.92361e-07
MA0140.10.0319303
MA0141.10.244275
MA0142.15.61005
MA0143.13.65134
MA0144.10.285324
MA0145.14.0804e-05
MA0146.16.17523e-09
MA0147.10.00324431
MA0148.11.20088
MA0149.10.00111095
MA0062.24.12482e-06
MA0035.20.279347
MA0039.23.82549e-13
MA0138.20.116541
MA0002.20.961613
MA0137.20.0501293
MA0104.20.000107514
MA0047.20.94572
MA0112.20.0511187
MA0065.22.05758e-05
MA0150.11.29912
MA0151.10
MA0152.10.0344826
MA0153.10.0963486
MA0154.10.113371
MA0155.10.000678493
MA0156.10.00364992
MA0157.10.813147
MA0158.10
MA0159.10.035257
MA0160.10.236607
MA0161.10
MA0162.19.49863e-15
MA0163.17.40164e-09
MA0164.10.0951929
MA0080.20.0667236
MA0018.20.495779
MA0099.218.396
MA0079.20
MA0102.20.366676
MA0258.10.00641429
MA0259.10.0102481
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
FOS#2353281.968302723820650.0003411936626312480.00346464996903694
JUN#3725181.75961660517230.01348784951926610.0476396738456705
JUND#3727291.584728549330150.007293398100102380.0301705233959121
NR3C1#2908212.456511640270580.0001182526080925830.00160621461003788



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

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