J Integr Bioinform - Nutrilyzer: a tool for deciphering atomic stoichiometry of differentially expressed paralogous proteins.

Tópicos

{ state(1844) use(1261) util(961) }
{ framework(1458) process(801) describ(734) }
{ sequenc(1873) structur(1644) protein(1328) }
{ gene(2352) biolog(1181) express(1162) }
{ bind(1733) structur(1185) ligand(1036) }
{ age(1611) year(1155) adult(843) }
{ method(1969) cluster(1462) data(1082) }
{ imag(1947) propos(1133) code(1026) }
{ data(1714) softwar(1251) tool(1186) }
{ blood(1257) pressur(1144) flow(957) }
{ spatial(1525) area(1432) region(1030) }
{ can(981) present(881) function(850) }
{ general(901) number(790) one(736) }
{ research(1085) discuss(1038) issu(1018) }
{ signal(2180) analysi(812) frequenc(800) }
{ activ(1452) weight(1219) physic(1104) }
{ can(774) often(719) complex(702) }
{ take(945) account(800) differ(722) }
{ treatment(1704) effect(941) patient(846) }
{ concept(1167) ontolog(924) domain(897) }
{ clinic(1479) use(1117) guidelin(835) }
{ extract(1171) text(1153) clinic(932) }
{ care(1570) inform(1187) nurs(1089) }
{ case(1353) use(1143) diagnosi(1136) }
{ perform(999) metric(946) measur(919) }
{ high(1669) rate(1365) level(1280) }
{ use(976) code(926) identifi(902) }
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{ method(2212) result(1239) propos(1039) }
{ model(3404) distribut(989) bayesian(671) }
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{ health(3367) inform(1360) care(1135) }
{ model(3480) simul(1196) paramet(876) }
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{ ehr(2073) health(1662) electron(1139) }
{ research(1218) medic(880) student(794) }
{ patient(2837) hospit(1953) medic(668) }
{ model(2656) set(1616) predict(1553) }
{ data(2317) use(1299) case(1017) }
{ medic(1828) order(1363) alert(1069) }
{ cost(1906) reduc(1198) effect(832) }
{ group(2977) signific(1463) compar(1072) }
{ sampl(1606) size(1419) use(1276) }
{ data(3008) multipl(1320) sourc(1022) }
{ first(2504) two(1366) second(1323) }
{ intervent(3218) particip(2042) group(1664) }
{ activ(1138) subject(705) human(624) }
{ time(1939) patient(1703) rate(768) }
{ patient(1821) servic(1111) care(1106) }
{ use(2086) technolog(871) perceiv(783) }
{ analysi(2126) use(1163) compon(1037) }
{ health(1844) social(1437) communiti(874) }
{ structur(1116) can(940) graph(676) }
{ cancer(2502) breast(956) screen(824) }
{ use(1733) differ(960) four(931) }
{ drug(1928) target(777) effect(648) }
{ result(1111) use(1088) new(759) }
{ implement(1333) system(1263) develop(1122) }
{ estim(2440) model(1874) function(577) }
{ decis(3086) make(1611) patient(1517) }
{ process(1125) use(805) approach(778) }
{ detect(2391) sensit(1101) algorithm(908) }

Resumo

Organisms try to maintain homeostasis by balanced uptake of nutrients from their environment. From an atomic perspective this means that, for example, carbon:nitrogen:sulfur ratios are kept within given limits. Upon limitation of, for example, sulfur, its acquisition is triggered. For yeast it was shown that transporters and enzymes involved in sulfur uptake are encoded as paralogous genes that express different isoforms. Sulfur deprivation leads to up-regulation of isoforms that are poor in sulfur-containing amino acids, that is, methinone and cysteine. Accordingly, sulfur-rich isoforms are down-regulated. We developed a web-based software, doped Nutrilyzer, that extracts paralogous protein coding sequences from an annotated genome sequence and evaluates their atomic composition. When fed with gene-expression data for nutrient limited and normal conditions, Nutrilyzer provides a list of genes that are significantly differently expressed and simultaneously contain significantly different amounts of the limited nutrient in their atomic composition. Its intended use is in the field of ecological stoichiometry. Nutrilyzer is available at http://nutrilyzer.hs-mittweida.de. Here we describe the work flow and results with an example from a whole-genome Arabidopsis thaliana gene-expression analysis upon oxygen deprivation. 43 paralogs distributed over 37 homology clusters were found to be significantly differently expressed while containing significantly different amounts of oxygen.

Resumo Limpo

organ tri maintain homeostasi balanc uptak nutrient environ atom perspect mean exampl carbonnitrogensulfur ratio kept within given limit upon limit exampl sulfur acquisit trigger yeast shown transport enzym involv sulfur uptak encod paralog gene express differ isoform sulfur depriv lead upregul isoform poor sulfurcontain amino acid methinon cystein accord sulfurrich isoform downregul develop webbas softwar dope nutrilyz extract paralog protein code sequenc annot genom sequenc evalu atom composit fed geneexpress data nutrient limit normal condit nutrilyz provid list gene signific differ express simultan contain signific differ amount limit nutrient atom composit intend use field ecolog stoichiometri nutrilyz avail httpnutrilyzerhsmittweidad describ work flow result exampl wholegenom arabidopsi thaliana geneexpress analysi upon oxygen depriv paralog distribut homolog cluster found signific differ express contain signific differ amount oxygen

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