Coexpression cluster:C525: Difference between revisions
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Latest revision as of 11:24, 17 September 2013
Full id: C525_tubular_vagina_cervix_rectum_Placental_colon_Hair
Phase1 CAGE Peaks
Hg19::chr10:4007246..4007251,+ | p@chr10:4007246..4007251 + |
Hg19::chr11:65144695..65144697,- | p@chr11:65144695..65144697 - |
Hg19::chr14:102027518..102027524,- | p@chr14:102027518..102027524 - |
Hg19::chr14:102027537..102027598,- | p@chr14:102027537..102027598 - |
Hg19::chr14:102027607..102027620,- | p@chr14:102027607..102027620 - |
Hg19::chr14:102027691..102027715,- | p@chr14:102027691..102027715 - |
Hg19::chr16:1128952..1128957,+ | p4@SSTR5 |
Hg19::chr16:1129001..1129004,+ | p6@SSTR5 |
Hg19::chr20:42980646..42980651,+ | p@chr20:42980646..42980651 + |
Hg19::chr21:36208874..36208890,+ | p@chr21:36208874..36208890 + |
Hg19::chr21:36208893..36208906,+ | p@chr21:36208893..36208906 + |
Hg19::chr2:109605543..109605554,- | p4@EDAR |
Hg19::chr2:109605568..109605573,- | p6@EDAR |
Hg19::chr2:109605588..109605606,- | p2@EDAR |
Hg19::chr4:93623257..93623261,+ | p@chr4:93623257..93623261 + |
Hg19::chr6:137365402..137365416,- | p8@IL20RA |
Hg19::chr7:45928212..45928215,+ | p14@IGFBP1 |
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 ID | GO name | FDR corrected p-value |
---|---|---|
GO:0065008 | regulation of biological quality | 0.0119799206895422 |
GO:0007431 | salivary gland development | 0.0124043961038235 |
GO:0004994 | somatostatin receptor activity | 0.0124043961038235 |
GO:0042346 | positive regulation of NF-kappaB import into nucleus | 0.0124043961038235 |
GO:0035272 | exocrine system development | 0.0124043961038235 |
GO:0042993 | positive regulation of transcription factor import into nucleus | 0.0124043961038235 |
GO:0050796 | regulation of insulin secretion | 0.0124043961038235 |
GO:0042307 | positive regulation of protein import into nucleus | 0.0124043961038235 |
GO:0046824 | positive regulation of nucleocytoplasmic transport | 0.0124043961038235 |
GO:0051222 | positive regulation of protein transport | 0.0124043961038235 |
GO:0042345 | regulation of NF-kappaB import into nucleus | 0.0124043961038235 |
GO:0042348 | NF-kappaB import into nucleus | 0.0124043961038235 |
GO:0065007 | biological regulation | 0.0124043961038235 |
GO:0030073 | insulin secretion | 0.0124043961038235 |
GO:0042593 | glucose homeostasis | 0.0124043961038235 |
GO:0033500 | carbohydrate homeostasis | 0.0124043961038235 |
GO:0022404 | molting cycle process | 0.0124043961038235 |
GO:0001942 | hair follicle development | 0.0124043961038235 |
GO:0022405 | hair cycle process | 0.0124043961038235 |
GO:0042633 | hair cycle | 0.0124043961038235 |
GO:0042303 | molting cycle | 0.0124043961038235 |
GO:0046883 | regulation of hormone secretion | 0.0124043961038235 |
GO:0002790 | peptide secretion | 0.0124043961038235 |
GO:0042475 | odontogenesis of dentine-containing teeth | 0.0124043961038235 |
GO:0030072 | peptide hormone secretion | 0.0124043961038235 |
GO:0042990 | regulation of transcription factor import into nucleus | 0.0124043961038235 |
GO:0042991 | transcription factor import into nucleus | 0.0124043961038235 |
GO:0042306 | regulation of protein import into nucleus | 0.0124043961038235 |
GO:0033157 | regulation of intracellular protein transport | 0.0124043961038235 |
GO:0004872 | receptor activity | 0.0127727213189944 |
GO:0042476 | odontogenesis | 0.0127727213189944 |
GO:0032386 | regulation of intracellular transport | 0.0127727213189944 |
GO:0051223 | regulation of protein transport | 0.0138701117521645 |
GO:0046822 | regulation of nucleocytoplasmic transport | 0.0139423432406483 |
GO:0046879 | hormone secretion | 0.0158756554137676 |
GO:0051050 | positive regulation of transport | 0.0166232626728935 |
GO:0005520 | insulin-like growth factor binding | 0.0166232626728935 |
GO:0015833 | peptide transport | 0.0166232626728935 |
GO:0004871 | signal transducer activity | 0.0166232626728935 |
GO:0060089 | molecular transducer activity | 0.0166232626728935 |
GO:0048732 | gland development | 0.0180796828083034 |
GO:0009653 | anatomical structure morphogenesis | 0.0180796828083034 |
GO:0008188 | neuropeptide receptor activity | 0.0181876457184049 |
GO:0042923 | neuropeptide binding | 0.0181876457184049 |
GO:0051046 | regulation of secretion | 0.0214033011731342 |
GO:0003001 | generation of a signal involved in cell-cell signaling | 0.0248296422928927 |
GO:0045177 | apical part of cell | 0.0298348531050072 |
GO:0019838 | growth factor binding | 0.0302283557850762 |
GO:0006606 | protein import into nucleus | 0.0316777496862145 |
GO:0051170 | nuclear import | 0.0316777496862145 |
GO:0007596 | blood coagulation | 0.0316777496862145 |
GO:0050817 | coagulation | 0.0316777496862145 |
GO:0007165 | signal transduction | 0.0316777496862145 |
GO:0007599 | hemostasis | 0.0316777496862145 |
GO:0051049 | regulation of transport | 0.0325756316374623 |
GO:0007187 | G-protein signaling, coupled to cyclic nucleotide second messenger | 0.0340193783461287 |
GO:0019935 | cyclic-nucleotide-mediated signaling | 0.0342424189330173 |
GO:0017038 | protein import | 0.0342424189330173 |
GO:0050878 | regulation of body fluid levels | 0.0344852227673087 |
GO:0042060 | wound healing | 0.0350398057358722 |
GO:0007154 | cell communication | 0.0350398057358722 |
GO:0008544 | epidermis development | 0.0353904821731165 |
GO:0030594 | neurotransmitter receptor activity | 0.0353904821731165 |
GO:0050794 | regulation of cellular process | 0.0353904821731165 |
GO:0042165 | neurotransmitter binding | 0.0353904821731165 |
GO:0007398 | ectoderm development | 0.0353904821731165 |
GO:0001653 | peptide receptor activity | 0.0353904821731165 |
GO:0008528 | peptide receptor activity, G-protein coupled | 0.0353904821731165 |
GO:0006913 | nucleocytoplasmic transport | 0.0362248593712815 |
GO:0051169 | nuclear transport | 0.0362248593712815 |
GO:0001558 | regulation of cell growth | 0.0370784581505363 |
GO:0048856 | anatomical structure development | 0.0372283652565221 |
GO:0004888 | transmembrane receptor activity | 0.0373534571022978 |
GO:0050789 | regulation of biological process | 0.038333343120518 |
GO:0016049 | cell growth | 0.0429041116610036 |
GO:0040008 | regulation of growth | 0.0429041116610036 |
GO:0008361 | regulation of cell size | 0.0432464846577091 |
GO:0042277 | peptide binding | 0.0432464846577091 |
GO:0006605 | protein targeting | 0.0447321235486876 |
GO:0016021 | integral to membrane | 0.0449080317908855 |
GO:0008285 | negative regulation of cell proliferation | 0.0449080317908855 |
GO:0031224 | intrinsic to membrane | 0.0449080317908855 |
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>disease_data<br>
Ontology term | p-value | n |
---|---|---|
epithelial cell of pancreas | 5.56e-26 | 4 |
Ontology term | p-value | n |
---|---|---|
tubular adenocarcinoma | 2.74e-50 | 2 |
pancreatic cancer | 5.56e-26 | 4 |
endocrine gland cancer | 7.67e-18 | 6 |
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) |
---|---|
MA0003.1 | 2.44612 |
MA0004.1 | 0.221943 |
MA0006.1 | 0.112549 |
MA0007.1 | 1.77009 |
MA0009.1 | 0.621697 |
MA0014.1 | 0.154351 |
MA0017.1 | 0.137108 |
MA0019.1 | 0.340029 |
MA0024.1 | 0.525161 |
MA0025.1 | 0.747404 |
MA0027.1 | 2.20546 |
MA0028.1 | 0.122394 |
MA0029.1 | 0.542771 |
MA0030.1 | 0.532314 |
MA0031.1 | 1.19386 |
MA0038.1 | 0.302644 |
MA0040.1 | 0.548121 |
MA0041.1 | 1.2374 |
MA0042.1 | 0.608306 |
MA0043.1 | 0.621991 |
MA0046.1 | 0.611559 |
MA0048.1 | 0.345177 |
MA0050.1 | 0.609862 |
MA0051.1 | 0.299199 |
MA0052.1 | 0.551663 |
MA0055.1 | 1.42965 |
MA0056.1 | 0 |
MA0057.1 | 0.0616251 |
MA0058.1 | 0.153757 |
MA0059.1 | 0.465036 |
MA0060.1 | 0.422819 |
MA0061.1 | 0.997605 |
MA0063.1 | 0 |
MA0066.1 | 0.302992 |
MA0067.1 | 0.924196 |
MA0068.1 | 0.111262 |
MA0069.1 | 0.607975 |
MA0070.1 | 0.597583 |
MA0071.1 | 0.746772 |
MA0072.1 | 0.593415 |
MA0073.1 | 0.360965 |
MA0074.1 | 2.24263 |
MA0076.1 | 0.493997 |
MA0077.1 | 0.586275 |
MA0078.1 | 0.382364 |
MA0081.1 | 0.152999 |
MA0083.1 | 0.628701 |
MA0084.1 | 1.10674 |
MA0087.1 | 0.591148 |
MA0088.1 | 1.04103 |
MA0089.1 | 0 |
MA0090.1 | 0.174619 |
MA0091.1 | 0.223914 |
MA0092.1 | 0.570207 |
MA0093.1 | 0.114388 |
MA0095.1 | 0 |
MA0098.1 | 0 |
MA0100.1 | 0.314026 |
MA0101.1 | 1.22726 |
MA0103.1 | 0.706501 |
MA0105.1 | 0.7537 |
MA0106.1 | 0.33677 |
MA0107.1 | 0.936151 |
MA0108.2 | 0.471286 |
MA0109.1 | 0 |
MA0111.1 | 0.184188 |
MA0113.1 | 0.350573 |
MA0114.1 | 0.537797 |
MA0115.1 | 0.850405 |
MA0116.1 | 0.949722 |
MA0117.1 | 0.656858 |
MA0119.1 | 1.39041 |
MA0122.1 | 0.681203 |
MA0124.1 | 0.810546 |
MA0125.1 | 0.730403 |
MA0130.1 | 0 |
MA0131.1 | 0.398042 |
MA0132.1 | 0 |
MA0133.1 | 0 |
MA0135.1 | 0.650071 |
MA0136.1 | 0.30842 |
MA0139.1 | 1.3388 |
MA0140.1 | 0.269307 |
MA0141.1 | 0.462123 |
MA0142.1 | 0.445733 |
MA0143.1 | 0.350722 |
MA0144.1 | 0.231909 |
MA0145.1 | 0.838342 |
MA0146.1 | 1.81242 |
MA0147.1 | 0.0784275 |
MA0148.1 | 0.240905 |
MA0149.1 | 0.261654 |
MA0062.2 | 0.0377014 |
MA0035.2 | 0.740647 |
MA0039.2 | 0.750837 |
MA0138.2 | 0.997372 |
MA0002.2 | 0.0459391 |
MA0137.2 | 0.398112 |
MA0104.2 | 0.188874 |
MA0047.2 | 0.326636 |
MA0112.2 | 0.08608 |
MA0065.2 | 0.211898 |
MA0150.1 | 0.170499 |
MA0151.1 | 0 |
MA0152.1 | 0.274535 |
MA0153.1 | 0.714423 |
MA0154.1 | 0.48172 |
MA0155.1 | 2.5589 |
MA0156.1 | 0.12788 |
MA0157.1 | 1.08073 |
MA0158.1 | 0 |
MA0159.1 | 0.571105 |
MA0160.1 | 0.252705 |
MA0161.1 | 0 |
MA0162.1 | 0.259032 |
MA0163.1 | 1.7822 |
MA0164.1 | 0.361105 |
MA0080.2 | 0.366978 |
MA0018.2 | 0.337929 |
MA0099.2 | 0.27482 |
MA0079.2 | 1.05686 |
MA0102.2 | 1.14323 |
MA0258.1 | 0.0605489 |
MA0259.1 | 0.591641 |
MA0442.1 | 0 |
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 | #promoters | Enrichment | p-value | q-value |
---|---|---|---|---|
FOXA1#3169 | 6 | 3.91108932331251 | 0.00277869454389008 | 0.0152218242575052 |
FOXA2#3170 | 5 | 7.24425404490154 | 0.00045226648015411 | 0.0042057037593104 |
MAFF#23764 | 3 | 9.9380040864609 | 0.00315701286110089 | 0.0165719373844248 |
NR3C1#2908 | 5 | 4.40383039152148 | 0.00416198804232154 | 0.0198318217516206 |
RXRA#6256 | 4 | 4.72343932685489 | 0.00868395261593973 | 0.0330001574521024 |
SETDB1#9869 | 4 | 9.48706498306129 | 0.00069418209031199 | 0.00559497479009831 |
SMC3#9126 | 7 | 6.19497234791352 | 6.13164858570721e-05 | 0.00100531121921927 |
TBP#6908 | 10 | 2.18045334535082 | 0.00564921492164463 | 0.0255145458052951 |
TCF7L2#6934 | 8 | 5.06831838265287 | 6.20084288736012e-05 | 0.00101585855735373 |
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.