Summary: Nuclear receptor-interacting protein 1 repression 3
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NRIP1 Edit Wikipedia article
|, RIP140, nuclear receptor interacting protein 1, CAKUT3|
|Nuclear receptor-interacting protein 1 repression 1|
|Nuclear receptor-interacting protein 1 repression 2|
|Nuclear receptor-interacting protein 1 repression 3|
|Nuclear receptor-interacting protein 1 repression 4|
Nuclear receptor interacting protein 1 (NRIP1) is a nuclear protein that specifically interacts with the hormone-dependent activation domain AF2 of nuclear receptors. Also known as RIP140, this protein is a key regulator which modulates transcriptional activity of a variety of transcription factors, including the estrogen receptor.
RIP140 has an important role in regulating lipid and glucose metabolism, and regulates gene expression in metabolic tissues including heart, skeletal muscle, and liver. A major role for RIP140 in adipose tissue is to block the expression of genes involved in energy dissipation and mitochondrial uncoupling, including uncoupling protein 1 and carnitine palmitoyltransferase 1b.
Estrogen-related receptor alpha (ERRa) can activate RIP140 during adipogenesis, by means of directly binding to an estrogen receptor element/ERR element and indirectly through Sp1 binding to the proximal promoter.
Knockout mice (females) are also infertile because they fail to ovulate. Failure of ovulation in these mice is caused by lack of cumulus expansion and altered expression of various genes, including amphiregulin, in ovarian follicles.
Levels of RIP140 expression in various tissues varies during aging in mice, suggesting changes in metabolic function. RIP140 is implicated in certain human disease processes. In morbid obesity, RIP140 levels are down-regulated in visceral adipose tissue. In breast cancer, RIP140 is involved in regulation of E2F1, an oncogene which discriminates between luminal and basal types of tumours. RIP140 has an influence upon cancer phenotype and prognosis. In addition, RIP140 has a role in inflammation, since it acts as a coactivator for NFkappaB/RelA-dependent cytokine gene expression. Lack of RIP140 leads to an inhibition of proinflammatory pathways in macrophages.
NRIP1 has been shown to interact with:
- GRCh38: Ensembl release 89: ENSG00000180530 - Ensembl, May 2017
- GRCm38: Ensembl release 89: ENSMUSG00000048490 - Ensembl, May 2017
- "Human PubMed Reference:". National Center for Biotechnology Information, U.S. National Library of Medicine.
- "Mouse PubMed Reference:". National Center for Biotechnology Information, U.S. National Library of Medicine.
- Cavailles V, Dauvois S, L'Horset F, Lopez G, Hoare S, Kushner PJ, Parker MG (Sep 1995). "Nuclear factor RIP140 modulates transcriptional activation by the estrogen receptor". EMBO J. 14 (15): 3741â€“51. doi:10.1002/j.1460-2075.1995.tb00044.x. PMC 394449. PMID 7641693.
- Katsanis N, Ives JH, Groet J, Nizetic D, Fisher EM (Apr 1998). "Localisation of receptor interacting protein 140 (RIP140) within 100 kb of D21S13 on 21q11, a gene-poor region of the human genome". Hum Genet. 102 (2): 221â€“3. doi:10.1007/s004390050682. PMID 9521594.
- "Entrez Gene: NRIP1 nuclear receptor interacting protein 1".
- Rosell M, Jones MC, Parker MG (2010). "Role of nuclear receptor corepressor RIP140 in metabolic syndrome". Biochim Biophys Acta. 1812 (8): 919â€“28. doi:10.1016/j.bbadis.2010.12.016. PMC 3117993. PMID 21193034.
- Fritah A, Steel JH, Nichol D, Parker N, Williams S, Price A, Strauss L, Ryder TA, Mobberley MA, Poutanen M, Parker M, White R (2010). "Elevated expression of the metabolic regulator receptor-interacting protein 140 results in cardiac hypertrophy and impaired cardiac function". Cardiovasc Res. 86 (3): 443â€“451. doi:10.1093/cvr/cvp418. PMC 2868176. PMID 20083575.
- Seth A, Steel JH, Nichol D, Pocock V, Kumaran MK, Fritah A, Mobberley M, Ryder TA, Rowlerson A, Scott J, Poutanen M, White R, Parker M (Sep 2007). "The transcriptional corepressor RIP140 regulates oxidative metabolism in skeletal muscle". Cell Metab. 6 (3): 236â€“245. doi:10.1016/j.cmet.2007.08.004. PMC 2680991. PMID 17767910.
- Herzog B, Hallberg M, Seth A, Woods A, White R, Parker MG (Nov 2007). "The nuclear receptor cofactor, receptor-interacting protein 140, is required for the regulation of hepatic lipid and glucose metabolism by liver X receptor". Mol Endocrinol. 21 (11): 2687â€“97. doi:10.1210/ME.2007-0213. PMC 2140279. PMID 17684114.
- Debevec D, Christian M, Morganstein D, Seth A, Herzog B, Parker M, White R (July 2007). "Receptor interacting protein 140 regulates expression of uncoupling protein 1 in adipocytes through specific peroxisome proliferator activated receptor isoforms and estrogen-related receptor alpha". Mol. Endocrinol. 21 (7): 1581â€“92. doi:10.1210/me.2007-0103. PMC 2072047. PMID 17456798.
- Nichol D, Christian M, Steel JH, White R, Parker MG (Oct 2006). "RIP140 expression is stimulated by estrogen-related receptor alpha during adipogenesis". J Biol Chem. 281 (43): 32140â€“32147. doi:10.1074/jbc.M604803200. PMID 16923809.
- Powelka AM, Seth A, Virbasius JV, Kiskinis E, Nicoloro SM, Guilherme A, Tang X, Straubhaar J, Cherniack AD, Parker MG, Czech MP (2006). "Suppression of oxidative metabolism and mitochondrial biogenesis by the transcriptional corepressor RIP140 in mouse adipocytes". J Clin Invest. 116 (1): 125â€“136. doi:10.1172/JCI26040. PMC 1319222. PMID 16374519.
- Leonardsson G, Steel JH, Christian M, Pocock V, Milligan S, Bell J, So PW, Medina-Gomez G, Vidal-Puig A, White R, Parker MG (May 2004). "Nuclear receptor corepressor RIP140 regulates fat accumulation". Proc Natl Acad Sci U S A. 101 (22): 8437â€“42. doi:10.1073/pnas.0401013101. PMC 420412. PMID 15155905.
- White R, Leonardsson G, Rosewell I, Ann Jacobs M, Milligan S, Parker M (Dec 2000). "The nuclear receptor co-repressor nrip1 (RIP140) is essential for female fertility". Nat. Med. 6 (12): 1368â€“74. doi:10.1038/82183. PMID 11100122.
- Tullet JM, Pocock V, Steel JH, White R, Milligan S, Parker MG (2005). "Multiple Signaling Defects in the Absence of RIP140 Impair Both Cumulus Expansion and Follicle Rupture". Endocrinology. 146 (9): 4127â€“4137. doi:10.1210/EN.2005-0348. PMID 15919748.
- Nautiyal J, Steel JH, Rosell MM, Nikolopoulou E, Lee K, Demayo FJ, White R, Richards JS, Parker MG (2010). "The nuclear receptor cofactor receptor-interacting protein 140 is a positive regulator of amphiregulin expression and cumulus cell-oocyte complex expansion in the mouse ovary". Endocrinology. 151 (6): 2923â€“2932. doi:10.1210/EN.2010-0081. PMC 2875814. PMID 20308529.
- "A common denominator of inflammations and fatty liver". News. Science Centric. 2008-05-31. Retrieved 2008-08-31.[dead link]
- Diaz MB, Krones-Herzig A, Metzger D, Ziegler A, Vegiopoulos A, Klingenspor M, MÃ¼ller-Decker K, Herzig S (April 2008). "Nuclear receptor cofactor receptor interacting protein 140 controls hepatic triglyceride metabolism during wasting in mice". Hepatology. 48 (3): 782â€“791. doi:10.1002/hep.22383. PMID 18712775.
- Ghosh S, Thakur MK (2008). "Tissue-specific expression of receptor-interacting protein in aging mouse". Age (Dordr). 30 (4): 237â€“243. doi:10.1007/s11357-008-9062-3. PMC 2585652. PMID 19424847.
- CatalÃ¡n V, GÃ³mez-Ambrosi J, Lizanzu A, RodrÃguez A, Silva C, Rotellar F, Gil MJ, Cienfuegos JA, Salvador J, FrÃ¼hbeck G (2009). "RIP140 gene and protein expression levels are downregulated in visceral adipose tissue in human morbid obesity". Obes Surg. 19 (6): 771â€“776. doi:10.1007/s11695-009-9834-6. PMID 19367438.
- Docquier A, Harmand PO, Fritsch S, Chanrion M, Darbon JM, CavaillÃ¨s V (2010). "The transcriptional coregulator RIP140 represses E2F1 activity and discriminates breast cancer subtypes". Clin Cancer Res. 16 (11): 2959â€“2970. doi:10.1158/1078-0432.CCR-09-3153. PMC 3112174. PMID 20410059.
- Zschiedrich I, Hardeland U, Krones-Herzig A, Berriel DM, Vegiopoulos A, MÃ¼ggenburg J, Sombroek D, Hofmann TG, Zawatzky R, Yu X, Gretz N, Christian M, White R, Parker MG, Herzig S (2008). "Coactivator function of RIP140 for NFkappaB/RelA-dependent cytokine gene expression". Blood. 112 (2): 264â€“276. doi:10.1182/blood-2007-11-121699. PMID 18469200.
- Kumar MB, Tarpey RW, Perdew GH (Aug 1999). "Differential recruitment of coactivator RIP140 by Ah and estrogen receptors. Absence of a role for LXXLL motifs". J. Biol. Chem. 274 (32): 22155â€“64. doi:10.1074/jbc.274.32.22155. PMID 10428779.
- Castet A; Boulahtouf Abdelhay; Versini GwennaÃ«lle; Bonnet Sandrine; Augereau Patrick; Vignon FranÃ§oise; Khochbin Saadi; Jalaguier StÃ©phan; CavaillÃ¨s Vincent (2004). "Multiple domains of the Receptor-Interacting Protein 140 contribute to transcription inhibition". Nucleic Acids Res. 32 (6): 1957â€“66. doi:10.1093/nar/gkh524. PMC 390375. PMID 15060175.
- Perissi V; Scafoglio Claudio; Zhang Jie; Ohgi Kenneth A; Rose David W; Glass Christopher K; Rosenfeld Michael G (Mar 2008). "TBL1 and TBLR1 phosphorylation on regulated gene promoters overcomes dual CtBP and NCoR/SMRT transcriptional repression checkpoints". Mol. Cell. 29 (6): 755â€“66. doi:10.1016/j.molcel.2008.01.020. PMC 2364611. PMID 18374649.
- Rual JF, Venkatesan K, Hao T, Hirozane-Kishikawa T, Dricot A, Li N, Berriz GF, Gibbons FD, Dreze M, Ayivi-Guedehoussou N, Klitgord N, Simon C, Boxem M, Milstein S, Rosenberg J, Goldberg DS, Zhang LV, Wong SL, Franklin G, Li S, Albala JS, Lim J, Fraughton C, Llamosas E, Cevik S, Bex C, Lamesch P, Sikorski RS, Vandenhaute J, Zoghbi HY, Smolyar A, Bosak S, Sequerra R, Doucette-Stamm L, Cusick ME, Hill DE, Roth FP, Vidal M (October 2005). "Towards a proteome-scale map of the human protein-protein interaction network". Nature. 437 (7062): 1173â€“8. doi:10.1038/nature04209. PMID 16189514.
- Sugawara T, Abe S, Sakuragi N, Fujimoto Y, Nomura E, Fujieda K, Saito M, Fujimoto S (August 2001). "RIP 140 modulates transcription of the steroidogenic acute regulatory protein gene through interactions with both SF-1 and DAX-1". Endocrinology. 142 (8): 3570â€“7. doi:10.1210/en.142.8.3570. PMID 11459805.
- Hu X; Chen Yixin; Farooqui Mariya; Thomas Mary C; Chiang Cheng-Ming; Wei Li-Na (Jan 2004). "Suppressive effect of receptor-interacting protein 140 on coregulator binding to retinoic acid receptor complexes, histone-modifying enzyme activity, and gene activation". J. Biol. Chem. 279 (1): 319â€“25. doi:10.1074/jbc.M307621200. PMID 14581481.
- Farooqui M; Franco Peter J; Thompson Jim; Kagechika Hiroyuki; Chandraratna Roshantha A S; Banaszak Len; Wei Li-Na (Feb 2003). "Effects of retinoid ligands on RIP140: molecular interaction with retinoid receptors and biological activity". Biochemistry. 42 (4): 971â€“9. doi:10.1021/bi020497k. PMID 12549917.
- L'Horset F, Dauvois S, Heery DM, CavaillÃ¨s V, Parker MG (Nov 1996). "RIP-140 interacts with multiple nuclear receptors by means of two distinct sites". Mol. Cell. Biol. 16 (11): 6029â€“36. doi:10.1128/MCB.16.11.6029. PMC 231605. PMID 8887632.
- ThÃ©not S, Henriquet C, Rochefort H, CavaillÃ¨s V (May 1997). "Differential interaction of nuclear receptors with the putative human transcriptional coactivator hTIF1". J. Biol. Chem. 272 (18): 12062â€“8. doi:10.1074/jbc.272.18.12062. PMID 9115274.
- Zilliacus J, Holter E, Wakui H, Tazawa H, Treuter E, Gustafsson JA (Apr 2001). "Regulation of glucocorticoid receptor activity by 14--3-3-dependent intracellular relocalization of the corepressor RIP140". Mol. Endocrinol. 15 (4): 501â€“11. doi:10.1210/mend.15.4.0624. PMID 11266503.
- Tazawa H; Osman Waffa; Shoji Yutaka; Treuter Eckardt; Gustafsson Jan-Ake; Zilliacus Johanna (Jun 2003). "Regulation of subnuclear localization is associated with a mechanism for nuclear receptor corepression by RIP140". Mol. Cell. Biol. 23 (12): 4187â€“98. doi:10.1128/MCB.23.12.4187-4198.2003. PMC 156128. PMID 12773562.
- Subramaniam N, Treuter E, Okret S (Jun 1999). "Receptor interacting protein RIP140 inhibits both positive and negative gene regulation by glucocorticoids". J. Biol. Chem. 274 (25): 18121â€“7. doi:10.1074/jbc.274.25.18121. PMID 10364267.
- Mellgren G; BÃ¸rud Bente; Hoang Tuyen; Yri Olav Erich; Fladeby Cathrine; Lien Ernst AsbjÃ¸rn; Lund Johan (May 2003). "Characterization of receptor-interacting protein RIP140 in the regulation of SF-1 responsive target genes". Mol. Cell. Endocrinol. 203 (1â€“2): 91â€“103. doi:10.1016/S0303-7207(03)00097-2. PMID 12782406.
- Detlav IE (1976). "[Anti-brain antibodies in serum and cerebrospinal fluid following cranio-cerebral trauma]". Zhurnal Nevropatologii I Psikhiatrii Imeni S.S. Korsakova (Moscow, Russia : 1952). 76 (3): 344â€“8. PMID 1266503.
- L'Horset F, Dauvois S, Heery DM, et al. (1996). "RIP-140 interacts with multiple nuclear receptors by means of two distinct sites". Mol. Cell. Biol. 16 (11): 6029â€“36. doi:10.1128/MCB.16.11.6029. PMC 231605. PMID 8887632.
- Yan ZH, Karam WG, Staudinger JL, et al. (1998). "Regulation of peroxisome proliferator-activated receptor alpha-induced transactivation by the nuclear orphan receptor TAK1/TR4". J. Biol. Chem. 273 (18): 10948â€“57. doi:10.1074/jbc.273.18.10948. PMID 9556573.
- Treuter E, Albrektsen T, Johansson L, et al. (1998). "A regulatory role for RIP140 in nuclear receptor activation". Mol. Endocrinol. 12 (6): 864â€“81. doi:10.1210/mend.12.6.0123. PMID 9626662.
- Eng FC, Barsalou A, Akutsu N, et al. (1998). "Different classes of coactivators recognize distinct but overlapping binding sites on the estrogen receptor ligand binding domain". J. Biol. Chem. 273 (43): 28371â€“7. doi:10.1074/jbc.273.43.28371. PMID 9774463.
- Lee CH, Chinpaisal C, Wei LN (1998). "Cloning and characterization of mouse RIP140, a corepressor for nuclear orphan receptor TR2". Mol. Cell. Biol. 18 (11): 6745â€“55. doi:10.1128/mcb.18.11.6745. PMC 109258. PMID 9774688.
- Miyata KS, McCaw SE, Meertens LM, et al. (1999). "Receptor-interacting protein 140 interacts with and inhibits transactivation by, peroxisome proliferator-activated receptor alpha and liver-X-receptor alpha". Mol. Cell. Endocrinol. 146 (1â€“2): 69â€“76. doi:10.1016/S0303-7207(98)00196-8. PMID 10022764.
- Subramaniam N, Treuter E, Okret S (1999). "Receptor interacting protein RIP140 inhibits both positive and negative gene regulation by glucocorticoids". J. Biol. Chem. 274 (25): 18121â€“7. doi:10.1074/jbc.274.25.18121. PMID 10364267.
- Wiebel FF, Steffensen KR, Treuter E, et al. (1999). "Ligand-independent coregulator recruitment by the triply activatable OR1/retinoid X receptor-alpha nuclear receptor heterodimer". Mol. Endocrinol. 13 (7): 1105â€“18. doi:10.1210/me.13.7.1105. PMID 10406462.
- Kumar MB, Tarpey RW, Perdew GH (1999). "Differential recruitment of coactivator RIP140 by Ah and estrogen receptors. Absence of a role for LXXLL motifs". J. Biol. Chem. 274 (32): 22155â€“64. doi:10.1074/jbc.274.32.22155. PMID 10428779.
- Hattori M, Fujiyama A, Taylor TD, et al. (2000). "The DNA sequence of human chromosome 21". Nature. 405 (6784): 311â€“9. doi:10.1038/35012518. PMID 10830953.
- Wei LN, Hu X, Chandra D, et al. (2001). "Receptor-interacting protein 140 directly recruits histone deacetylases for gene silencing". J. Biol. Chem. 275 (52): 40782â€“7. doi:10.1074/jbc.M004821200. PMID 11006275.
- Zilliacus J, Holter E, Wakui H, et al. (2001). "Regulation of glucocorticoid receptor activity by 14--3-3-dependent intracellular relocalization of the corepressor RIP140". Mol. Endocrinol. 15 (4): 501â€“11. doi:10.1210/mend.15.4.0624. PMID 11266503.
- Mal A, Sturniolo M, Schiltz RL, et al. (2001). "A role for histone deacetylase HDAC1 in modulating the transcriptional activity of MyoD: inhibition of the myogenic program". EMBO J. 20 (7): 1739â€“53. doi:10.1093/emboj/20.7.1739. PMC 145490. PMID 11285237.
- Vo N, Fjeld C, Goodman RH (2001). "Acetylation of nuclear hormone receptor-interacting protein RIP140 regulates binding of the transcriptional corepressor CtBP". Mol. Cell. Biol. 21 (18): 6181â€“8. doi:10.1128/MCB.21.18.6181-6188.2001. PMC 87335. PMID 11509661.
- Zennaro MC, Souque A, Viengchareun S, et al. (2002). "A new human MR splice variant is a ligand-independent transactivator modulating corticosteroid action". Mol. Endocrinol. 15 (9): 1586â€“98. doi:10.1210/mend.15.9.0689. PMID 11518808.
- Chen Y, Kerimo A, Khan S, Wei LN (2003). "Real-time analysis of molecular interaction of retinoid receptors and receptor-interacting protein 140 (RIP140)". Mol. Endocrinol. 16 (11): 2528â€“37. doi:10.1210/me.2002-0124. PMID 12403842.
- NRIP1 protein, human at the US National Library of Medicine Medical Subject Headings (MeSH)
- NURSA C258
- PDBe-KB provides an overview of all the structure information available in the PDB for Human Nuclear receptor-interacting protein 1 (NRIP1)
This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.
Nuclear receptor-interacting protein 1 repression 3 Provide feedback
This domain is the third repression domain of nuclear receptor-interacting protein 1 [1-2].
Christian M, Tullet JM, Parker MG;, J Biol Chem. 2004;279:15645-15651.: Characterization of four autonomous repression domains in the corepressor receptor interacting protein 140. PUBMED:14736873 EPMC:14736873
Castet A, Boulahtouf A, Versini G, Bonnet S, Augereau P, Vignon F, Khochbin S, Jalaguier S, Cavailles V;, Nucleic Acids Res. 2004;32:1957-1966.: Multiple domains of the Receptor-Interacting Protein 140 contribute to transcription inhibition. PUBMED:15060175 EPMC:15060175
This tab holds annotation information from the InterPro database.
InterPro entry IPR031407Nuclear receptor-interacting protein 1 (also known as nuclear factor RIP140) modulates transcriptional activation by steroid receptors such as NR3C1, NR3C2 and ESR1 [PUBMED:7641693]. It also modulates transcriptional repression by nuclear hormone receptors [PUBMED:10364267] and clock gene expression [PUBMED:21628546]. It consists of four distinct autonomous repression domains [PUBMED:14736873].
Below is a listing of the unique domain organisations or architectures in which this domain is found. More...
The graphic that is shown by default represents the longest sequence with a given architecture. Each row contains the following information:
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This example describes an architecture with one
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We make a range of alignments for each Pfam-A family:
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- Representative Proteomes (RPs) at 15%, 35%, 55% and 75% co-membership thresholds
- alignment generated by searching the UniProtKB sequence database using the family HMM
- alignment generated by searching the NCBI sequence database using the family HMM
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You can see the alignments as HTML or in three different sequence viewers:
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We make a range of alignments for each Pfam-A family. You can see a description of each above. You can view these alignments in various ways but please note that some types of alignment are never generated while others may not be available for all families, most commonly because the alignments are too large to handle.
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key: available, not generated, — not available.
Format an alignment
We make all of our alignments available in Stockholm format. You can download them here as raw, plain text files or as gzip-compressed files.
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This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.
Note: You can also download the data file for the tree.
Curation and family details
This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.
|Number in seed:||10|
|Number in full:||94|
|Average length of the domain:||87.90 aa|
|Average identity of full alignment:||68 %|
|Average coverage of the sequence by the domain:||7.68 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 45638612 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||5|
|Download:||download the raw HMM for this family|
Weight segments by...
Change the size of the sunburst
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- 0 sequences
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This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the More....
This chart is a modified "sunburst" visualisation of the species tree for this family. It shows each node in the tree as a separate arc, arranged radially with the superkingdoms at the centre and the species arrayed around the outermost ring.
How the sunburst is generated
The tree is built by considering the taxonomic lineage of each sequence that has a match to this family. For each node in the resulting tree, we draw an arc in the sunburst. The radius of the arc, its distance from the root node at the centre of the sunburst, shows the taxonomic level ("superkingdom", "kingdom", etc). The length of the arc represents either the number of sequences represented at a given level, or the number of species that are found beneath the node in the tree. The weighting scheme can be changed using the sunburst controls.
In order to reduce the complexity of the representation, we reduce the number of taxonomic levels that we show. We consider only the following eight major taxonomic levels:
Colouring and labels
Segments of the tree are coloured approximately according to their superkingdom. For example, archeal branches are coloured with shades of orange, eukaryotes in shades of purple, etc. The colour assignments are shown under the sunburst controls. Where space allows, the name of the taxonomic level will be written on the arc itself.
As you move your mouse across the sunburst, the current node will be highlighted. In the top section of the controls panel we show a summary of the lineage of the currently highlighed node. If you pause over an arc, a tooltip will be shown, giving the name of the taxonomic level in the title and a summary of the number of sequences and species below that node in the tree.
Anomalies in the taxonomy tree
There are some situations that the sunburst tree cannot easily handle and for which we have work-arounds in place.
Missing taxonomic levels
Some species in the taxonomic tree may not have one or more of the main eight levels that we display. For example, Bos taurus is not assigned an order in the NCBI taxonomic tree. In such cases we mark the omitted level with, for example, "No order", in both the tooltip and the lineage summary.
Unmapped species names
The tree is built by looking at each sequence in the full alignment for the family. We take the name of the species given by UniProt and try to map that to the full taxonomic tree from NCBI. In some cases, the name chosen by UniProt does not map to any node in the NCBI tree, perhaps because the chosen name is listed as a synonym or a misspelling in the NCBI taxonomy.
So that these nodes are not simply omitted from the sunburst tree, we group them together in a separate branch (or segment of the sunburst tree). Since we cannot determine the lineage for these unmapped species, we show all levels between the superkingdom and the species as "uncategorised".
Since we reduce the species tree to only the eight main taxonomic levels, sequences that are mapped to the sub-species level in the tree would not normally be shown. Rather than leave out these species, we map them instead to their parent species. So, for example, for sequences belonging to one of the Vibrio cholerae sub-species in the NCBI taxonomy, we show them instead as belonging to the species Vibrio cholerae.
Too many species/sequences
For large species trees, you may see blank regions in the outer layers of the sunburst. These occur when there are large numbers of arcs to be drawn in a small space. If an arc is less than approximately one pixel wide, it will not be drawn and the space will be left blank. You may still be able to get some information about the species in that region by moving your mouse across the area, but since each arc will be very small, it will be difficult to accurately locate a particular species.
The tree shows the occurrence of this domain across different species. More...
We show the species tree in one of two ways. For smaller trees we try to show an interactive representation, which allows you to select specific nodes in the tree and view them as an alignment or as a set of Pfam domain graphics.
Unfortunately we have found that there are problems viewing the interactive tree when the it becomes larger than a certain limit. Furthermore, we have found that Internet Explorer can become unresponsive when viewing some trees, regardless of their size. We therefore show a text representation of the species tree when the size is above a certain limit or if you are using Internet Explorer to view the site.
If you are using IE you can still load the interactive tree by clicking the "Generate interactive tree" button, but please be aware of the potential problems that the interactive species tree can cause.
For all of the domain matches in a full alignment, we count the number that are found on all sequences in the alignment. This total is shown in the purple box.
We also count the number of unique sequences on which each domain is found, which is shown in green. Note that a domain may appear multiple times on the same sequence, leading to the difference between these two numbers.
Finally, we group sequences from the same organism according to the NCBI code that is assigned by UniProt, allowing us to count the number of distinct sequences on which the domain is found. This value is shown in the pink boxes.
We use the NCBI species tree to group organisms according to their taxonomy and this forms the structure of the displayed tree. Note that in some cases the trees are too large (have too many nodes) to allow us to build an interactive tree, but in most cases you can still view the tree in a plain text, non-interactive representation. Those species which are represented in the seed alignment for this domain are highlighted.
You can use the tree controls to manipulate how the interactive tree is displayed:
- show/hide the summary boxes
- highlight species that are represented in the seed alignment
- expand/collapse the tree or expand it to a given depth
- select a sub-tree or a set of species within the tree and view them graphically or as an alignment
- save a plain text representation of the tree
Please note: for large trees this can take some time. While the tree is loading, you can safely switch away from this tab but if you browse away from the family page entirely, the tree will not be loaded.