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Coexpression cluster:C139

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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>uberon_data<br><br>


Cell Type
Ontology termp-valuen
embryonic cell4.72e-13248
ectodermal cell4.88e-1071
epithelial cell7.61e-10254
neurectodermal cell1.25e-0759
non-terminally differentiated cell1.53e-07180
Uber Anatomy
Ontology termp-valuen
ectoderm-derived structure6.58e-19169
ectoderm2.48e-18173
presumptive ectoderm2.48e-18173
head8.21e-18123
anterior region of body1.24e-17129
craniocervical region1.24e-17129
multi-cellular organism2.57e-17659
organism subdivision6.85e-15365
anatomical system2.65e-14625
anatomical group5.98e-14626
central nervous system7.81e-1482
regional part of nervous system1.81e-1294
nervous system1.81e-1294
neural plate2.63e-1286
presumptive neural plate2.63e-1286
embryo8.02e-12612
pre-chordal neural plate8.62e-1261
neurectoderm1.32e-1190
cell layer2.68e-11312
epithelium4.46e-11309
neural tube5.34e-1157
neural rod5.34e-1157
future spinal cord5.34e-1157
neural keel5.34e-1157
embryonic structure1.13e-10605
developing anatomical structure1.13e-10605
germ layer2.22e-10604
embryonic tissue2.22e-10604
presumptive structure2.22e-10604
epiblast (generic)2.22e-10604
brain3.17e-1069
future brain3.17e-1069
regional part of forebrain6.05e-1041
forebrain6.05e-1041
future forebrain6.05e-1041
anatomical cluster9.89e-10286
organ part1.05e-09219
regional part of brain1.71e-0959
gray matter2.34e-0934
brain grey matter2.34e-0934
telencephalon3.37e-0934
cerebral hemisphere4.00e-0932
anterior neural tube4.03e-0942
regional part of telencephalon5.51e-0933
anatomical conduit8.45e-09241
cerebral cortex2.05e-0825
pallium2.05e-0825
tube3.08e-08194
organ1.03e-07511
multi-tissue structure4.75e-07347
external genitalia6.03e-0722
reproductive organ9.38e-0748
gonad9.78e-0721
indifferent external genitalia9.78e-0721
indifferent gonad9.78e-0721
gonad primordium9.78e-0721


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)

{{{tfbs_overrepresentation_jaspar}}}



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