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genewikijamboree

genewikijamboree

A place to ask questions and otherwise communicate about the Gene Wiki Jamboree.
genewikijamboree
AndrewGNF: fix name (according to http://predictioncenter.org/index...) [[Image:Target3dsmRib 354predictedModels CASP8.jpg|thumb|right|250px| A target structure (ribbons) and 354 template-based predictions superimposed (gray Calpha backbones); from CASP8]] '''CASP''', which stands for '''Critical Assessment of protein Structure Prediction''', is a community-wide, worldwide experiment for [[protein structure prediction]] taking place every two years since 1994.<ref>{{cite journal |author=Moult, J., ''et al.'' |year=1995 |title=A large-scale experiment to assess protein structure prediction methods |journal=Proteins |volume=23 |issue=3 |pages=ii–iv }}</ref> CASP provides research groups with an opportunity to objectively test their structure prediction methods and delivers an independent assessment of the state of the art in protein structure modeling to the research community and software users. Even though the primary goal of CASP is to help advance the methods of identifying... - Andrew Su
genewikijamboree
AndrewGNF: AndrewGNF moved page Mir-155 to MiR-155: more accepted name <!-- EDIT BELOW THIS LINE --> {{Infobox rfam | Name = miR-155 | image = MiR-155 secondary structure.png| width = 220px | caption = miR-155 secondary structure and sequence conservation. | Symbol = miR-155 | AltSymbols = | Rfam = RF00731 | miRBase_family = MIPF0000157 | RNA_type = [[microRNA]] | Tax_domain = ''[[Eukaryote|Eukaryota]];'' | HGNCid = | OMIM = }} {{PBB|geneid=406947}} '''MiR-155''' is a [[microRNA]] that in humans is encoded by the ''MIR155'' host [[gene]] or ''MIR155HG''.<ref name="entrez"/> MiR-155 plays an important role in various [[physiology|physiological]] and [[pathology|pathological]] processes. [[Exogenous]] molecular control ''[[in vivo]]'' of miR-155 expression could restrain [[malignant]] growth and [[virus|viral]] infections, or to attenuate the progression of [[cardiovascular]] diseases. == MicroRNA background == [[MicroRNA]]s (miRNAs) are small (20–25 nucleotides) non-coding RNAs... - Andrew Su
genewikijamboree
AndrewGNF: clean up {{PBB|geneid=1}} '''Alpha-1-B glycoprotein''' is a [[protein]] in humans that is encoded by the A1BG [[gene]]. <ref name="entrez"> {{cite web | title = Entrez Gene: Alpha-1-B glycoprotein | url = http://www.ncbi.nlm.nih.gov/sites... | accessdate = 2012-11-09T15:55:33.609951-08:00 }}</ref> The protein encoded by this gene is a plasma glycoprotein of unknown function. The protein shows sequence similarity to the variable regions of some immunoglobulin supergene family member proteins. [provided by RefSeq, Jul 2008]. == References == {{reflist}} {{gene-19-stub}}
genewikijamboree
List of sequenced eukaryotic genomes - http://en.wikipedia.org/wiki...
AndrewGNF: incomplete is an understatement {{Expand list|date=November 2012}} <!--Suggestion: Sort the tables by date instead of the relatively irrelevant Latin name alphabetical order.--> [[Image:S cerevisiae under DIC microscopy.jpg|right|thumb|180px|''[[Saccharomyces cerevisiae]]'' was the first eukaryotic organism to have its complete genome sequence determined.]] This '''list of sequenced eukaryotic genomes''' contains all the [[eukaryote]]s known to have publicly available complete [[Cell nucleus|nuclear]] and [[organelle]] [[genome sequence]]s that have been assembled, annotated and published; draft genomes are not included, nor are organelle-only sequences. [[DNA]] was first sequenced in 1977. The first free-living organism to have its genome completely sequenced was the bacterium ''[[Haemophilus influenzae]]'', in 1995. In 1996 ''[[Saccharomyces cerevisiae]]'' (baker's yeast) was the first eukaryote genome sequence to be released and in 1998 the first genome sequence for a...
genewikijamboree
AndrewGNF: mergeto Sirtuin 1; we should consolidate all info in model organisms under the human SIRT1 entry... {{mergeto|Sirtuin 1}} '''Sir2''' (whose [[homology (biology)|homolog]] in [[mammal]]s is known as '''SIRT1''', '''SIR2L1''' or '''Sir2α''') was the first gene of the [[sirtuin]] genes to be found. It was found in [[budding yeast]], and, since then, members of this [[Conservation (genetics)|highly conserved]] family have been found in nearly all organisms studied.<ref name="Pp">{{cite journal |last1=Frye |first1=R |title=Phylogenetic Classification of Prokaryotic and Eukaryotic Sir2-like Proteins |journal=Biochemical and Biophysical Research Communications |volume=273 |issue=2 |pages=793–8 |year=2000 |pmid=10873683 |doi=10.1006/bbrc.2000.3000}}</ref> Sirtuins are hypothesized to play a key role in an organism's response to stresses (such as heat or starvation) and to be responsible for the lifespan-extending effects of [[calorie restriction]].<ref name=sinclair>{{cite journal...
genewikijamboree
Intrinsically unstructured proteins - http://en.wikipedia.org/wiki...
AndrewGNF: /* Disorder and Disease */ wikilink [[File:PDB 2fft EBI.jpg|thumb|An ensemble of NMR structures of the Thylakoid soluble phosphoprotein TSP9, which shows a largely flexible protein chain.<ref name="pmid17176085">{{cite journal |author=Song J, Lee MS, Carlberg I, Vener AV, Markley JL |title=Micelle-induced folding of spinach thylakoid soluble phosphoprotein of 9 kDa and its functional implications |journal=Biochemistry |volume=45 |issue=51 |pages=15633–43 |year=2006 |month=December |pmid=17176085 |pmc=2533273 |doi=10.1021/bi062148m |url=}}</ref>|250px]] '''Intrinsically unstructured proteins''', often referred to as ''naturally unfolded proteins'' or ''disordered proteins'', are [[proteins]] characterized by lack of stable [[tertiary structure]] when the protein exists as an isolated polypeptide chain (a [[Protein subunit|subunit]]) under physiological conditions [[in vitro]].<ref>{{cite journal |author=Dyson HJ, Wright PE |title=Intrinsically unstructured proteins and their...
genewikijamboree
Qazi-Markouizos syndrome - http://en.wikipedia.org/wiki...
AndrewGNF: init '''Qazi-Markouizos syndrome''' is a rare hereditary condition characterized by [[hypotonia]], [[congenital fiber type disproportion]] and dysharmonic skeletal maturation.<ref>{{cite journal|last=Qazi|first=QH|coauthors=Markouizos, D; Rao, C; Sheikh, T; Beller, E; Kula, R|title=A syndrome of hypotonia, psychomotor retardation, seizures, delayed and dysharmonic skeletal maturation, and congenital fibre type disproportion.|journal=Journal of medical genetics|date=1994 May|volume=31|issue=5|pages=405-9|pmid=8064821}}</ref><ref>{{cite journal|last=Poznanski|first=AK|coauthors=Garn, SM; Kuhns, LR; Sandusky, ST|title=Dysharmonic maturation of the hand in the congenital malformation syndromes.|journal=American journal of physical anthropology|date=1971 Nov|volume=35|issue=3|pages=417-32|pmid=4332712}}</ref> ==References== {{reflist}} ==External links== * [http://www.orpha.net/consor... Orphanet] * {{OMIM|600096}}
genewikijamboree
Qazi–Markouizos syndrome - http://en.wikipedia.org/wiki...
AndrewGNF: init '''Qazi-Markouizos syndrome''' is a rare hereditary condition characterized by [[hypotonia]], [[congenital fiber type disproportion]] and dysharmonic skeletal maturation.<ref>{{cite journal|last=Qazi|first=QH|coauthors=Markouizos, D; Rao, C; Sheikh, T; Beller, E; Kula, R|title=A syndrome of hypotonia, psychomotor retardation, seizures, delayed and dysharmonic skeletal maturation, and congenital fibre type disproportion.|journal=Journal of medical genetics|date=1994 May|volume=31|issue=5|pages=405-9|pmid=8064821}}</ref><ref>{{cite journal|last=Poznanski|first=AK|coauthors=Garn, SM; Kuhns, LR; Sandusky, ST|title=Dysharmonic maturation of the hand in the congenital malformation syndromes.|journal=American journal of physical anthropology|date=1971 Nov|volume=35|issue=3|pages=417-32|pmid=4332712}}</ref> ==References== {{reflist}} ==External links== * [http://www.orpha.net/consor... Orphanet] * {{OMIM|600096}}
genewikijamboree
Pulmonary surfactant-associated protein A1 - http://en.wikipedia.org/wiki...
I9606: /* Gene */ {{PBB|geneid=6435}} '''Pulmonary surfactant-associated protein A1''' (PSP-A), also known as '''surfactant protein A1''' (SFTPA1) is a [[protein]] that in humans is encoded by the ''SFTPA1'' [[gene]]. The protein encoded by this gene (SP-A1) is primarily synthesized in lung alveolar type II cells (see [[type II pneumocyte]]), as part of a complex of lipids and proteins known as [[pulmonary surfactant]]. The function of this complex is to reduce [[surface tension]] in the [[alveolus]] and prevent collapse during [[expiration]]. The protein component of surfactant helps in the modulation of the innate immune response, and inflammatory processes. SP-A1 is a member of a subfamily of C-type [[lectins]] called [[collectin]]s. Together with SP-A2 (see [[SFTPA2]]), they are the most abundant proteins of [[pulmonary surfactant]]. SP-A1 binds to the [[carbohydrates]] found in the surface of several [[microorganisms]] and helps in the defense against respiratory pathogens. ==...
genewikijamboree
Pulmonary surfactant-associated protein A1 - http://en.wikipedia.org/w...
I9606: /* Gene */ {{PBB|geneid=6435}} '''Pulmonary surfactant-associated protein A1''' (PSP-A), also known as '''surfactant protein A1''' (SFTPA1) is a [[protein]] that in humans is encoded by the ''SFTPA1'' [[gene]]. The protein encoded by this gene (SP-A1) is primarily synthesized in lung alveolar type II cells (see [[type II pneumocyte]]), as part of a complex of lipids and proteins known as [[pulmonary surfactant]]. The function of this complex is to reduce [[surface tension]] in the [[alveolus]] and prevent collapse during [[expiration]]. The protein component of surfactant helps in the modulation of the innate immune response, and inflammatory processes. SP-A1 is a member of a subfamily of C-type [[lectins]] called [[collectin]]s. Together with SP-A2 (see [[SFTPA2]]), they are the most abundant proteins of [[pulmonary surfactant]]. SP-A1 binds to the [[carbohydrates]] found in the surface of several [[microorganisms]] and helps in the defense against respiratory pathogens. ==...
genewikijamboree
I9606: copy edit for relevance to biology In [[machine learning]] and [[statistics]], '''feature selection''', also known as '''variable selection''', '''feature reduction''', '''attribute selection''' or '''variable subset selection''', is the technique of selecting a subset of relevant features for building robust learning models. Feature selection is a particularly important step in analyzing the data from many experimental techniques in biology, such as [[DNA microarray]]s, because of they often entail a large number of measured variables (features) but a very low number of samples. By removing most irrelevant and redundant features from the data, feature selection helps improve the performance of learning models by: :* Alleviating the effect of the [[curse of dimensionality]]. :* Enhancing generalization capability. :* Speeding up learning process. :* Improving model interpretability. Feature selection also helps people to acquire better understanding about their data by telling...
genewikijamboree
Feature selection - http://en.wikipedia.org/w...
I9606: copy edit for relevance to biology In [[machine learning]] and [[statistics]], '''feature selection''', also known as '''variable selection''', '''feature reduction''', '''attribute selection''' or '''variable subset selection''', is the technique of selecting a subset of relevant features for building robust learning models. Feature selection is a particularly important step in analyzing the data from many experimental techniques in biology, such as [[DNA microarray]]s, because of they often entail a large number of measured variables (features) but a very low number of samples. By removing most irrelevant and redundant features from the data, feature selection helps improve the performance of learning models by: :* Alleviating the effect of the [[curse of dimensionality]]. :* Enhancing generalization capability. :* Speeding up learning process. :* Improving model interpretability. Feature selection also helps people to acquire better understanding about their data by telling...
genewikijamboree
I9606: minor presentation alteration {{PBB|geneid=94}} '''Serine/threonine-protein kinase receptor R3''' is an [[enzyme]] that in humans is encoded by the ''ACVRL1'' [[gene]].<ref name="pmid8397373">{{cite journal | author = ten Dijke P, Ichijo H, Franzen P, Schulz P, Saras J, Toyoshima H, Heldin CH, Miyazono K | title = Activin receptor-like kinases: a novel subclass of cell-surface receptors with predicted serine/threonine kinase activity | journal = Oncogene | volume = 8 | issue = 10 | pages = 2879–87 | year = 1993 | month = Oct | pmid = 8397373 | pmc = | doi = }}</ref><ref name="pmid8640225">{{cite journal | author = Johnson DW, Berg JN, Baldwin MA, Gallione CJ, Marondel I, Yoon SJ, Stenzel TT, Speer M, Pericak-Vance MA, Diamond A, Guttmacher AE, Jackson CE, Attisano L, Kucherlapati R, Porteous ME, Marchuk DA | title = Mutations in the activin receptor-like kinase 1 gene in hereditary haemorrhagic telangiectasia type 2 | journal = Nat Genet | volume = 13 | issue = 2 | pages =...
genewikijamboree
I9606: minor presentation alteration {{PBB|geneid=94}} '''Serine/threonine-protein kinase receptor R3''' is an [[enzyme]] that in humans is encoded by the ''ACVRL1'' [[gene]].<ref name="pmid8397373">{{cite journal | author = ten Dijke P, Ichijo H, Franzen P, Schulz P, Saras J, Toyoshima H, Heldin CH, Miyazono K | title = Activin receptor-like kinases: a novel subclass of cell-surface receptors with predicted serine/threonine kinase activity | journal = Oncogene | volume = 8 | issue = 10 | pages = 2879–87 | year = 1993 | month = Oct | pmid = 8397373 | pmc = | doi = }}</ref><ref name="pmid8640225">{{cite journal | author = Johnson DW, Berg JN, Baldwin MA, Gallione CJ, Marondel I, Yoon SJ, Stenzel TT, Speer M, Pericak-Vance MA, Diamond A, Guttmacher AE, Jackson CE, Attisano L, Kucherlapati R, Porteous ME, Marchuk DA | title = Mutations in the activin receptor-like kinase 1 gene in hereditary haemorrhagic telangiectasia type 2 | journal = Nat Genet | volume = 13 | issue = 2 | pages =...
genewikijamboree
AndrewGNF: merge to Cyclin-dependent kinase 9? {{mergeto|Cyclin-dependent kinase 9}} [[Image:RNA_polymerase_II_elongation_control.jpg|thumb|300px|right|'''Figure 1. RNA polymerase II elongation control. '''Pol II comes under the control of negative elongation factors (DSIF and NELF) shortly after initiation. P-TEFb mediates a transition into productive elongation by phosphorylating the two negative factors and the polymerase and is regulated by association with the 7SK snRNP.]] The positive transcription elongation factor, '''P-TEFb''', plays an essential role in the regulation of transcription by [[RNA polymerase II]] (Pol II) in eukaryotes.<ref>Zhou Q, Li T, Price DH. RNA Polymerase II Elongation Control. Annu Rev Biochem 2012.</ref> Immediately following initiation Pol II becomes trapped in promoter proximal paused positions on the majority of human genes (Figure 1).<ref>Rahl PB, Lin CY, Seila AC, Flynn RA, McCuine S, Burge CB, et al. c-Myc regulates transcriptional pause release....
genewikijamboree
I9606: formatting {{PBB|geneid=5300}} '''Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1''' is an [[enzyme]] that in humans is encoded by the ''PIN1'' [[gene]].<ref name="pmid8606777">{{cite journal | author = Lu KP, Hanes SD, Hunter T | title = A human peptidyl-prolyl isomerase essential for regulation of mitosis | journal = Nature | volume = 380 | issue = 6574 | pages = 544–7 | date=May 1996| pmid = 8606777 | pmc = | doi = 10.1038/380544a0 }}</ref><ref>{{cite web | title = Entrez Gene: PIN1 Protein (peptidylprolyl cis/trans isomerase) NIMA-interacting 1| url = http://www.ncbi.nlm.nih.gov/sites... accessdate = }}</ref> (Not to be confused with (Pin-formed 1), an [[auxin]] transporter in [[Arabidopsis thaliana]].) '''Pin 1''', or peptidyl-prolyl cis/trans [[isomerase]] (PPIase), isomerizes only phospho-Serine/Threonine-Proline [[sequence motif|motifs]]. The enzyme binds to a subset of proteins and thus plays a role as a post...
genewikijamboree
I9606: removing disambiguation template {{PBB|geneid=5300}} '''Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1''' is an [[enzyme]] that in humans is encoded by the ''PIN1'' [[gene]].<ref name="pmid8606777">{{cite journal | author = Lu KP, Hanes SD, Hunter T | title = A human peptidyl-prolyl isomerase essential for regulation of mitosis | journal = Nature | volume = 380 | issue = 6574 | pages = 544–7 | date=May 1996| pmid = 8606777 | pmc = | doi = 10.1038/380544a0 }}</ref><ref>{{cite web | title = Entrez Gene: PIN1 Protein (peptidylprolyl cis/trans isomerase) NIMA-interacting 1| url = http://www.ncbi.nlm.nih.gov/sites... accessdate = }}</ref> Not to be confused with (Pin-formed 1), an [[auxin]] transporter in [[Arabidopsis thaliana]] '''Pin 1''', or peptidyl-prolyl cis/trans [[isomerase]] (PPIase), isomerizes only phospho-Serine/Threonine-Proline [[sequence motif|motifs]]. The enzyme binds to a subset of proteins and thus plays a...
genewikijamboree
I9606: merging content from other Pin1 article {{PBB|geneid=5300}} '''Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1''' is an [[enzyme]] that in humans is encoded by the ''PIN1'' [[gene]].<ref name="pmid8606777">{{cite journal | author = Lu KP, Hanes SD, Hunter T | title = A human peptidyl-prolyl isomerase essential for regulation of mitosis | journal = Nature | volume = 380 | issue = 6574 | pages = 544–7 | date=May 1996| pmid = 8606777 | pmc = | doi = 10.1038/380544a0 }}</ref><ref>{{cite web | title = Entrez Gene: PIN1 Protein (peptidylprolyl cis/trans isomerase) NIMA-interacting 1| url = http://www.ncbi.nlm.nih.gov/sites... accessdate = }}</ref> {{ distinguish2| (Pin-formed 1), an [[auxin]] transporter in [[Arabidopsis thaliana]]}} '''Pin 1''', or peptidyl-prolyl cis/trans [[isomerase]] (PPIase), isomerizes only phospho-Serine/Threonine-Proline [[sequence motif|motifs]]. The enzyme binds to a subset of proteins and thus plays...
genewikijamboree
I9606: merging content from other Pin1 article {{PBB|geneid=5300}} '''Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1''' is an [[enzyme]] that in humans is encoded by the ''PIN1'' [[gene]].<ref name="pmid8606777">{{cite journal | author = Lu KP, Hanes SD, Hunter T | title = A human peptidyl-prolyl isomerase essential for regulation of mitosis | journal = Nature | volume = 380 | issue = 6574 | pages = 544–7 | date=May 1996| pmid = 8606777 | pmc = | doi = 10.1038/380544a0 }}</ref><ref>{{cite web | title = Entrez Gene: PIN1 Protein (peptidylprolyl cis/trans isomerase) NIMA-interacting 1| url = http://www.ncbi.nlm.nih.gov/sites... accessdate = }}</ref> {{ distinguish2| (Pin-formed 1), an [[auxin]] transporter in [[Arabidopsis thaliana]]}} '''Pin 1''', or peptidyl-prolyl cis/trans [[isomerase]] (PPIase), isomerizes only phospho-Serine/Threonine-Proline [[sequence motif|motifs]]. The enzyme binds to a subset of proteins and thus plays...
genewikijamboree
I9606: merging with other article on human PIN1 (capital PIN1 seems to be the official gene symbol now according to HGNC) #REDIRECT [[PIN1]]
genewikijamboree
I9606: merging with other article on human PIN1 (capital PIN1 seems to be the official gene symbol now according to HGNC) #REDIRECT [[PIN1]]
genewikijamboree
I9606: added pbb box (merge from MIR155 article) - mostly empty now, but will fill automatically as more is discovered.) <!-- EDIT BELOW THIS LINE --> {{Infobox rfam | Name = mir-155 | image = MiR-155 secondary structure.png| width = 220px | caption = miR-155 secondary structure and sequence conservation. | Symbol = mir-155 | AltSymbols = | Rfam = RF00731 | miRBase_family = MIPF0000157 | RNA_type = [[microRNA]] | Tax_domain = ''[[Eukaryote|Eukaryota]];'' | HGNCid = | OMIM = }} {{PBB|geneid=406947}} [[MicroRNA]]s are non-coding RNAs ([[Non-coding RNA|ncRNAs]]) that regulate the expression levels of other genes through several mechanisms at a post transcriptional stage, they work by inactivating translation of gene or gene clusters or by degrading genes. About 30 percent of the eukaryotic genome is controlled by miRNAs, the estimated total number of miR genes is ~1000.<ref name="PMID15965474"/> They exert influences on cellular processes of proliferation, differentiation, apoptosis and...
genewikijamboree
I9606: merging with better developed article on same topic #REDIRECT [[Mir-155]]
genewikijamboree
I9606: merging with better developed article on same topic #REDIRECT [[Mir-155]]
genewikijamboree
I9606: added pbb box (merge from MIR155 article) - mostly empty now, but will fill automatically as more is discovered.) <!-- EDIT BELOW THIS LINE --> {{Infobox rfam | Name = mir-155 | image = MiR-155 secondary structure.png| width = 220px | caption = miR-155 secondary structure and sequence conservation. | Symbol = mir-155 | AltSymbols = | Rfam = RF00731 | miRBase_family = MIPF0000157 | RNA_type = [[microRNA]] | Tax_domain = ''[[Eukaryote|Eukaryota]];'' | HGNCid = | OMIM = }} {{PBB|geneid=406947}} [[MicroRNA]]s are non-coding RNAs ([[Non-coding RNA|ncRNAs]]) that regulate the expression levels of other genes through several mechanisms at a post transcriptional stage, they work by inactivating translation of gene or gene clusters or by degrading genes. About 30 percent of the eukaryotic genome is controlled by miRNAs, the estimated total number of miR genes is ~1000.<ref name="PMID15965474"/> They exert influences on cellular processes of proliferation, differentiation, apoptosis and...
genewikijamboree
I9606: ←Redirected page to Epoxide hydrolase 2 #REDIRECT [[Epoxide_hydrolase_2]]
genewikijamboree
I9606: ←Redirected page to Kinesin family member 11 #REDIRECT [[kinesin family member 11]]
genewikijamboree
I9606: ←Redirected page to N-acetyltransferase 1 #REDIRECT [[N-acetyltransferase_1]]
genewikijamboree
I9606: ←Redirected page to UGT1A7 (gene) #REDIRECT [[UGT1A7 (gene)]]
genewikijamboree
I9606: ←Redirected page to MHC class I polypeptide-related sequence A #REDIRECT [[MHC_class_I_polypeptide-related_sequence_A]]
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