Toward Pathway Engineering: a New Database of Genetic and Molecular

Total Page:16

File Type:pdf, Size:1020Kb

Toward Pathway Engineering: a New Database of Genetic and Molecular owrd thwy ingineeringX e xew htse of qeneti nd woleulr thwys winoru unehis snstitute for ghemil eserhD uyoto niversity ing of genes nd moleules is prom qenome eE sequening pro jets hve een lso rpidly expnding owing to ompleted for udding yest @IP quenes to puntions the dvnement of exp erimenE wpA nd for severl teri inE tl tehnologies in the rod luding ynoteri @QFT wpA he rumn qenome ro jet res of moleulr nd ellulr whih ws rried out y the ws initited in the lte IWVHs iologyF sn order to mke full uzus hxe eserh snstitute s nturl onsequene of use of the informtion otined in tpnF the tehnology developments in y genome pro jetsD it is essenE por the rst time in humn moleulr iology nd with the til tht suh funtionl dt history we re eginning to hve expettion of new iomedil re prop erly omputerized in the dt t hnd whih leds toE pplitionsF he pro jet will dtses nd informtis tehE wrd si understnding of unover the omplete hxe seE nologies re developed for funE quene of the humn genome the fundmentl prolems in life tionl preditionF onsisting of Q illion se pirs sienes inluding the origin nd nd IHH thousnd genesF sn evolution of life nd the onE prom qene qtlogs IWUUD smll virus genomeD eption nd developmentofn 0xIURD onsisting of just SDHHH individulF he dt will lso to thwys se pirs nd II genes ws deE stimulte prtil pplitions he funtionl dt tht relte termined y the emerging tehE in medilD phrmeutilD nd to sequene informtion re urE nology of hxe sequene deterE griulturl sienesF roweverD rently stored s nnottions to mintionF efter two dedes somewht ontrry to puli noE sequene dtD for exmpleD in of tehnology developments the tionD the sequene dt otined the soElled fetures tlesD in y genome pro jets do not y rst omplete genome of the sequene dtses of hxes themselves provide diret nE freeEliving iologil orgnismD nd proteinsF roweverD these swers to suh fundmentl proE remophilus inuenzeD ws deE silly represent the sequeneE lems or prtil pplitionsF termined in IWWSF he teriE funtion reltionships of single he sequening of genome is l genome onsisting of IFV milE moleulesD iFeFD the individul n esier prt thn the underE lion nuleotides nd IDUHH genes omp onents of iologil sysE stnding of funtionl impliE is lredy followed y the exE temD nd they do not ontin tions of whenD whereD nd how plosion of omplete genomi seE higher level informtionD iFeFD genes nd moleules funtion in quenes of numer of orgnE wiring digrmsD of geneti inE living orgnismsF portuntelyD isms from teri to eukryE tertions nd moleulr interE our knowledge of the funtionE otesF es of mid IWWTD the genome tionsF st is ovious tht withE tht is represented y wht is pthwysD lthough we intend out suh wiringEdigrms ioE termed inry reltionF en to omputerize other pthwysD logil system ould never e deE exp ert in the eld would syntheE suh s signl trnsdution nd sried or understo o dF size pthwy from olletion ell yle pthwys nd the of inry reltions otined y geneti pthwys of the erly e hve thus initited exp erimentl oservtionsF sn stges in fruit y developmentF pro jet nmed uiqqD uyoto order to op e with the rpidE e exp et tht one suh dt inylopedi of qenes nd ly expnding o dy of informE re prop erly omputerizedD it qenomesD to omputerize the tion it is neessry to omputE will eome fesile to ssist exE urrent knowledge of moleulr erize the pro ess of synthesizing p erimentsD filitte understndE nd ellulr iology in terms of pthwysD in ddition to omE ingD nd even p erform logiE the informtion pthwys tht puterizing known pthwys deE l simultions of informtion onsist of interting genes or rived y humn exp ertsF pthwys ontrolling ll sp ets moleulesF he si dt item of living orgnismsF in uiqq is pirwise interE gurrentlyD we re fo using tion of genes or moleules our ttention on the met oli pigure IX he home pge of the qenomexet server t httpXGGwwwFgenomeFdFjpG nd the hfqi nd uiqq serh windowsF qenomexet htse qenomexet under the qenome he im of qenomexet is not snformtis ro jetD prt of the simply network onnetionY it ervie rumn qenome rogrm of the is to estlish the informtis winistry of idutionD ieneD infrstruture for genome reE sn IWWI we estlished p orts nd gulture @wonushoAF serh nd relted reserh res omputer network nmed in moleulr nd ellulr ioloE ieneD the niversityofokyoD ed in the FF or iurop eF iven gyF sn view of the susequent hs gretly ontriuted towrd the dtses whih limed to government funding of snternet tht endF e orgnized in tpn tully tivities in tpnD we re only hevily dep end on the systems he most p opulr mo de urrently mintining the onE nd proto ols develop ed in other of ess to the qenomexet netion etween okyoD uyoto ountriesF dtse servie is to use our nd pukuokF yriginllyD we enE uiqq is n ttempt to dE server shown in pigF ID visioned network ommunity vne our originl onepts nd whih provides mong othersD where the informtis needs of tehnologiesD nd tul dt the hfqi integrted dtse individul reserhers nd indiE olletion eortsF elthough retrievl system nd the seE vidul pro jets would e relized we hve not yet mde forE quene interprettion to ols inE on their lo l mhines y inteE ml nnounement of uiqqD luding sequene similrity nd grting dtses nd omputE preliminry version hs een motif serh progrmsF he tionl resoures distriuted over pulily ville through the server reeives tens of thousnds the networkF e elieve tht the qenomexet server sine of queries p er dyD oneEthird of wideErnging dtse servie heemer IWWSF he trget dte whih re from rodF elE in qenomexetD whih is jointly of the rst relese of uiqq is though the qenomexet dtse provided y the up eromputer yto er IWWTF e pln to disE servie is result of tehnologE vortory of the snstitute for triute ompt diss in ddition il developments in tpnD for ghemil eserhD uyoto niE to the servie over the snternetF exmpleD hfqi ws develop ed versity nd the rumn qenome in my l ortoryD most of the genter of snstitute of wedil dtses tht we oer origintE Pathways Binary relations KEGG Hierarchies Genes Molecules LIGAND Genome OMIM DBGET CAS Databases DNA/Protein Databases Medline pigure PX he onept of uiqq nd its reltion to hfqiF sn uiqq funtionl sp ets of genes nd moleules re represented y inry reltionsD hierrhiesD nd pthwysF e retrieved uniformly nd links he gonepts he onept of reltion nd re mde etween relted entries dedution is thus the sis in dierent dtsesF sn this of our uiqq pro jetF por gurrentlyD uiqq is omp osed lo oselyEoupled integrtionD the our logiEsed tivitiesD we of three interonneted setionsX shem or the formt of hown knowledge the pst oll orE pthwysD genesD nd moleulesD entry is orgnized y dt items tions with the pifth qenertion whih re lso linked to is left to eh dtseF his gomputer ro jet tem memE numer of existing dtses should e ontrsted with using ers in sgy nd the reserhers through hfqi @pigF PAF the sme reltionl dtse nd in the qenome snformtis eE foth oneptully nd prE enforing unied shem for serh ro jets IWWIEIWWS nd tillyD uiqq nd hfqi entries oming from mny dierE IWWTEPHHHF re tightly oupled systemsF ent souresD whih neessrily inE hfqi provides n integrted volves the pro ess of dt onE view of vrious dtses in he ehnologies versionF moleulr iologyD where the E he prolifertion of sis of integrtion is the link @iE uiqq mkes full use of the ws o on to our pproh nry reltionA etween relted dvnements in the dtse of lo ose integrtionY the link entries in dierent dtsesF sn nd networking tehnologyD inE pilities of hfqi t the uiqqD n orgnism my e luding dedutive nd o jetE mehnism of very nieE onsidered dtse of genes oriented dtsesD the multimeE lyF he textEsed hfqi sysE nd gene pro dutsD nd the link di environment of D nd tem ws esily extended to the etween them is used for synE the moile gentD tvF elE multimedi environmentD where thesizing pthwyF husD though we mintin the logiE Qh grphisD Ph grphisD nd oth uiqq nd hfqi onE sed formlism of reltion nd imges re now retrievle in tin n sp et of the dedutive dedutionD we tke prtilD the version of hfqiF dtse where new reltions exile pproh in the tul sn dditionD euse the up dte n e dedued from reltions implementtionF por exmpleD pro edure do es not involve dt stored in the dtseF we use the gyev dedutive onversionD hfqi hs een enother imp ortnt onept dtse system for exp erimentE nd will ontinue to e le to in uiqq is the hierrhy tht ing the dedution pro essD ut op e with the ever inresing represents funtionlD struturlD in the tul implementtion of numer nd volume of dily upE nd evolutionry reltionships of uiqq we hve developed our dted dtsesF genes nd moleulesF por exE own gCC lirry for mnipultE uiqq inherits ll these mpleD the degree of similrity ing inry reltions nd hierrE hfqi pilitiesF purtherE in sequenes nd Qh strutures hiesF moreD the grphis hndling of of proteins is used for lssifyE ith similr philosophyD pthwy digrms nd hromoE ing sup erfmilies nd Qh foldsF hfqi do es not dep end on some mps hs een implementE he txonomy is the lssiE ny dtse mngement sysE ed y tvF he new pilities tion of orgnismsD whih is imE temF he entire system hs of logil inferene nd simulE portnt in extending sequene een developed in houseF etuE tion re still under developmentD nd Qh struturl similrities to llyD hfqi hs its ro ots in the ut we hop e to mke the rst funtionl similritiesF hese shie sequene nlysis pkE test version ville shortlyF nd other lssitions re tkE ge tht s developed in the erly en from pproprite soures nd IWVHs in the FF xtionl snstiE implemented in uiqqF tutes of relthF hfqi ims t ht golletion ifE integrting dierent dtses hile the inry reltion nd dierent types of dt
Recommended publications
  • The Kyoto Encyclopedia of Genes and Genomes (KEGG)
    Kyoto Encyclopedia of Genes and Genome Minoru Kanehisa Institute for Chemical Research, Kyoto University HFSPO Workshop, Strasbourg, November 18, 2016 The KEGG Databases Category Database Content PATHWAY KEGG pathway maps Systems information BRITE BRITE functional hierarchies MODULE KEGG modules KO (KEGG ORTHOLOGY) KO groups for functional orthologs Genomic information GENOME KEGG organisms, viruses and addendum GENES / SSDB Genes and proteins / sequence similarity COMPOUND Chemical compounds GLYCAN Glycans Chemical information REACTION / RCLASS Reactions / reaction classes ENZYME Enzyme nomenclature DISEASE Human diseases DRUG / DGROUP Drugs / drug groups Health information ENVIRON Health-related substances (KEGG MEDICUS) JAPIC Japanese drug labels DailyMed FDA drug labels 12 manually curated original DBs 3 DBs taken from outside sources and given original annotations (GENOME, GENES, ENZYME) 1 computationally generated DB (SSDB) 2 outside DBs (JAPIC, DailyMed) KEGG is widely used for functional interpretation and practical application of genome sequences and other high-throughput data KO PATHWAY GENOME BRITE DISEASE GENES MODULE DRUG Genome Molecular High-level Practical Metagenome functions functions applications Transcriptome etc. Metabolome Glycome etc. COMPOUND GLYCAN REACTION Funding Annual budget Period Funding source (USD) 1995-2010 Supported by 10+ grants from Ministry of Education, >2 M Japan Society for Promotion of Science (JSPS) and Japan Science and Technology Agency (JST) 2011-2013 Supported by National Bioscience Database Center 0.8 M (NBDC) of JST 2014-2016 Supported by NBDC 0.5 M 2017- ? 1995 KEGG website made freely available 1997 KEGG FTP site made freely available 2011 Plea to support KEGG KEGG FTP academic subscription introduced 1998 First commercial licensing Contingency Plan 1999 Pathway Solutions Inc.
    [Show full text]
  • Precise Generation of Systems Biology Models from KEGG Pathways Clemens Wrzodek*,Finjabuchel,¨ Manuel Ruff, Andreas Drager¨ and Andreas Zell
    Wrzodek et al. BMC Systems Biology 2013, 7:15 http://www.biomedcentral.com/1752-0509/7/15 METHODOLOGY ARTICLE OpenAccess Precise generation of systems biology models from KEGG pathways Clemens Wrzodek*,FinjaBuchel,¨ Manuel Ruff, Andreas Drager¨ and Andreas Zell Abstract Background: The KEGG PATHWAY database provides a plethora of pathways for a diversity of organisms. All pathway components are directly linked to other KEGG databases, such as KEGG COMPOUND or KEGG REACTION. Therefore, the pathways can be extended with an enormous amount of information and provide a foundation for initial structural modeling approaches. As a drawback, KGML-formatted KEGG pathways are primarily designed for visualization purposes and often omit important details for the sake of a clear arrangement of its entries. Thus, a direct conversion into systems biology models would produce incomplete and erroneous models. Results: Here, we present a precise method for processing and converting KEGG pathways into initial metabolic and signaling models encoded in the standardized community pathway formats SBML (Levels 2 and 3) and BioPAX (Levels 2 and 3). This method involves correcting invalid or incomplete KGML content, creating complete and valid stoichiometric reactions, translating relations to signaling models and augmenting the pathway content with various information, such as cross-references to Entrez Gene, OMIM, UniProt ChEBI, and many more. Finally, we compare several existing conversion tools for KEGG pathways and show that the conversion from KEGG to BioPAX does not involve a loss of information, whilst lossless translations to SBML can only be performed using SBML Level 3, including its recently proposed qualitative models and groups extension packages.
    [Show full text]
  • Table 1S. the KEGG Biochemical Pathways Categorization of LA Lily Unigenes Pathways
    Table 1S. The KEGG biochemical pathways categorization of LA lily unigenes pathways. KEGG Categories Mapped-KO Unigene-NUM Ratio of No. ALL pathway KO Pathway-ID Metabolic pathways 954 4337 8.66 2067 ko01100 Biosynthesis of secondary metabolites 403 2285 4.56 720 ko01110 Biosynthesis of antibiotics 206 1147 2.29 --- ko01130 Microbial metabolism in diverse environments 157 995 1.99 720 ko01120 Ribosome 122 504 1.01 142 ko03010 Spliceosome 107 502 1 115 ko03040 Biosynthesis of amino acids 105 614 1.23 --- ko01230 Carbon metabolism 104 707 1.41 --- ko01200 Oxidative phosphorylation 100 335 0.67 206 ko00190 Purine metabolism 100 386 0.77 237 ko00230 RNA transport 98 861 1.72 134 ko03013 Endocytosis 92 736 1.47 138 ko04144 Protein processing in endoplasmic reticulum 88 567 1.13 137 ko04141 homologous recombination 84 933 1.86 144 ko05169 Ubiquitin mediated proteolysis 78 396 0.79 119 ko04120 HTLV-I infection 76 367 0.73 199 ko05166 Pyrimidine metabolism 76 298 0.6 150 ko00240 Non-alcoholic fatty liver disease (NAFLD) 72 209 0.42 --- ko04932 PI3K-Akt signaling pathway 71 328 0.66 226 ko04151 Viral carcinogenesis 68 387 0.77 132 ko05203 Cell cycle 63 339 0.68 103 ko04110 Proteoglycans in cancer 58 229 0.46 --- ko05205 Regulation of actin cytoskeleton 58 234 0.47 144 ko04810 Ribosome biogenesis in eukaryotes 56 237 0.47 82 ko03008 Phagosome 54 280 0.56 93 ko04145 Focal adhesion 53 185 0.37 133 ko04510 Lysosome 53 253 0.51 99 ko04142 RNA degradation 53 305 0.61 70 ko03018 Herpes simplex infection 52 257 0.51 121 ko05168 Cell cycle - yeast 51 260
    [Show full text]
  • A Tool for Retrieving Pathway Genes from KEGG Pathway Database
    bioRxiv preprint doi: https://doi.org/10.1101/416131; this version posted September 13, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. KPGminer: A tool for retrieving pathway genes from KEGG pathway database A. K. M. Azad School of Biotechnology and Biomolecular Sciences, University of NSW, Chancellery Walk, Kensington, 2033, Australia Abstract Pathway analysis is a very important aspect in computational systems bi- ology as it serves as a crucial component in many computational pipelines. KEGG is one of the prominent databases that host pathway information associated with various organisms. In any pathway analysis pipelines, it is also important to collect and organize the pathway constituent genes for which a tool to automatically retrieve that would be a useful one to the practitioners. In this article, I present KPGminer, a tool that retrieves the constituent genes in KEGG pathways for various organisms and or- ganizes that information suitable for many downstream pathway analysis pipelines. We exploited several KEGG web services using REST APIs, par- ticularly GET and LIST methods to request for the information retrieval which is available for developers. Moreover, KPGminer can operate both for a particular pathway (single mode) or multiple pathways (batch mode). Next, we designed a crawler to extract necessary information from the re- sponse and generated outputs accordingly. KPGminer brings several key features including organism-specific and pathway-specific extraction of path- way genes from KEGG and always up-to-date information.
    [Show full text]
  • Downregulated Developmental Processes in the Postnatal Right
    www.nature.com/cddiscovery ARTICLE OPEN Downregulated developmental processes in the postnatal right ventricle under the influence of a volume overload ✉ ✉ ✉ Chunxia Zhou1,6, Sijuan Sun2,6, Mengyu Hu3, Yingying Xiao1, Xiafeng Yu1 , Lincai Ye 1,4,5 and Lisheng Qiu 1 © The Author(s) 2021 The molecular atlas of postnatal mouse ventricular development has been made available and cardiac regeneration is documented to be a downregulated process. The right ventricle (RV) differs from the left ventricle. How volume overload (VO), a common pathologic state in children with congenital heart disease, affects the downregulated processes of the RV is currently unclear. We created a fistula between the abdominal aorta and inferior vena cava on postnatal day 7 (P7) using a mouse model to induce a prepubertal RV VO. RNAseq analysis of RV (from postnatal day 14 to 21) demonstrated that angiogenesis was the most enriched gene ontology (GO) term in both the sham and VO groups. Regulation of the mitotic cell cycle was the second-most enriched GO term in the VO group but it was not in the list of enriched GO terms in the sham group. In addition, the number of Ki67-positive cardiomyocytes increased approximately 20-fold in the VO group compared to the sham group. The intensity of the vascular endothelial cells also changed dramatically over time in both groups. The Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis of the downregulated transcriptome revealed that the peroxisome proliferators-activated receptor (PPAR) signaling pathway was replaced by the cell cycle in the top-20 enriched KEGG terms because of the VO.
    [Show full text]
  • Transcriptome Analysis of the Regulatory Mechanism of Foxo on Wing Dimorphism in the Brown Planthopper, Nilaparvata Lugens (Hemiptera: Delphacidae)
    insects Article Transcriptome Analysis of the Regulatory Mechanism of FoxO on Wing Dimorphism in the Brown Planthopper, Nilaparvata lugens (Hemiptera: Delphacidae) Nan Xu 1, Sheng-Fei Wei 1 and Hai-Jun Xu 1,2,3,* 1 State Key Laboratory of Rice Biology, Zhejiang University, Hangzhou 310058, China; [email protected] (N.X.); [email protected] (S.-F.W.) 2 Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insect Pests, Zhejiang University, Hangzhou 310058, China 3 Institute of Insect Sciences, Zhejiang University, Hangzhou 310058, China * Correspondence: [email protected]; Tel.: +86-571-88982996 Simple Summary: The brown planthopper (BPH) Nilaparvata lugens can develop into either long- winged or short-winged adults depending on environmental stimuli received during larval stages. The transcription factor NlFoxO serves as a key regulator determining alternative wing morphs in BPH, but the underlying molecular mechanism is largely unknown. Here, we investigated the transcriptomic profile of forewing and hindwing buds across the 5th-instar stage, the wing-morph decision stage. Our results indicated that NlFoxO modulated the developmental plasticity of wing buds mainly by regulating the expression of cell proliferation-associated genes. Abstract: The brown planthopper (BPH), Nilaparvata lugens, can develop into either short-winged (SW) or long-winged (LW) adults according to environmental conditions, and has long served as a model organism for exploring the mechanisms of wing polyphenism in insects. The transcription Citation: Xu, N.; Wei, S.-F.; Xu, H.-J. factor NlFoxO acts as a master regulator that directs the development of either SW or LW morphs, Transcriptome Analysis of the but the underlying molecular mechanism is largely unknown.
    [Show full text]
  • "Using the KEGG Database Resource". In: Current Protocols in Bioinformatics
    Using the KEGG Database Resource UNIT 1.12 KEGG (Kyoto Encyclopedia of Genes and Genomes) is a bioinformatics resource for understanding biological function from a genomic perspective. It is a multispecies, integrated resource consisting of genomic, chemical, and network information with cross-references to numerous outside databases and containing a complete set of building blocks (genes and molecules) and wiring diagrams (biological pathways) to represent cellular functions (Kanehisa et al., 2004). In this unit, protocols are described for using the five major KEGG resources: PATHWAY, GENES, SSDB, EXPRESSION, and LIGAND. The KEGG PATHWAY database (see Basic Protocols 1 to 4) consists of a user-friendly tool for analyzing the network of protein and small-molecule interactions that occur in the cells of various organisms. KEGG GENES (see Basic Protocols 5 and 6) provides access to the collection of gene data organized so as to be accessible via text searches, from the PATHWAY database, or via cross-species orthology searches. The KEGG Sequence Similiarity Database (SSDB; see Basic Protocols 7 to 9) consists of a precomputed database of all-versus-all Smith- Waterman similarity scores among all genes in KEGG GENES, enabling relationships between homologs to be easily visualized on the pathway and genome maps or viewed as clusters of orthologous genes. The KEGG EXPRESSION database (see Basic Protocols 10 to 14) contains both data and tools for analyzing gene expression data. User-defined data such as microarray experiments may also be uploaded for analysis using the tools available in KEGG EXPRESSION. Finally, KEGG LIGAND (see Basic Protocols 16 to 19) is a database of small molecules, their structures, and information relating to the enzymes that act on them.
    [Show full text]
  • KEGG: Kyoto Encyclopedia of Genes and Genomes Hiroyuki Ogata, Susumu Goto, Kazushige Sato, Wataru Fujibuchi, Hidemasa Bono and Minoru Kanehisa*
    1999 Oxford University Press Nucleic Acids Research, 1999, Vol. 27, No. 1 29–34 KEGG: Kyoto Encyclopedia of Genes and Genomes Hiroyuki Ogata, Susumu Goto, Kazushige Sato, Wataru Fujibuchi, Hidemasa Bono and Minoru Kanehisa* Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan Received September 8, 1998; Revised September 22, 1998; Accepted October 14, 1998 ABSTRACT The basic concepts of KEGG (1) and underlying informatics technologies (2,3) have already been published. KEGG is tightly Kyoto Encyclopedia of Genes and Genomes (KEGG) is integrated with the LIGAND chemical database for enzyme a knowledge base for systematic analysis of gene reactions (4,5) as well as with most of the major molecular functions in terms of the networks of genes and biology databases by the DBGET/LinkDB system (6) under the molecules. The major component of KEGG is the Japanese GenomeNet service (7). The database organization PATHWAY database that consists of graphical dia- efforts require extensive analyses of completely sequenced grams of biochemical pathways including most of the genomes, as exemplified by the analyses of metabolic pathways known metabolic pathways and some of the known (8) and ABC transport systems (9). In this article, we describe the regulatory pathways. The pathway information is also current status of the KEGG databases and discuss the use of represented by the ortholog group tables summarizing KEGG for functional genomics. orthologous and paralogous gene groups among different organisms. KEGG maintains the GENES OBJECTIVES OF KEGG database for the gene catalogs of all organisms with complete genomes and selected organisms with In May 1995, we initiated the KEGG project under the Human partial genomes, which are continuously re-annotated, Genome Program of the Ministry of Education, Science, Sports as well as the LIGAND database for chemical com- and Culture in Japan.
    [Show full text]
  • RNA Seq Analyses of Chicken Reveals Biological Pathways Involved in Acclimation Into Diferent Geographical Locations Himansu Kumar1, Hyojun Choo2, Asankadyr U
    www.nature.com/scientificreports OPEN RNA seq analyses of chicken reveals biological pathways involved in acclimation into diferent geographical locations Himansu Kumar1, Hyojun Choo2, Asankadyr U. Iskender1,3, Krishnamoorthy Srikanth1, Hana Kim1, Asankadyr T. Zhunushov3, Gul Won Jang1, Youngjo Lim1, Ki‑Duk Song4 & Jong‑Eun Park1* Transcriptome expression refects genetic response in diverse conditions. In this study, RNA sequencing was utilized to profle multiple tissues such as liver, breast, caecum, and gizzard of Korean commercial chicken raised in Korea and Kyrgyzstan. We analyzed ten samples per tissue from each location to identify candidate genes which are involved in the adaptation of Korean commercial chicken to Kyrgyzstan. At false discovery rate (FDR) < 0.05 and fold change (FC) > 2, we found 315, 196, 167 and 198 genes in liver, breast, cecum, and gizzard respectively as diferentially expressed between the two locations. GO enrichment analysis showed that these genes were highly enriched for cellular and metabolic processes, catalytic activity, and biological regulations. Similarly, KEGG pathways analysis indicated metabolic, PPAR signaling, FoxO, glycolysis/gluconeogenesis, biosynthesis, MAPK signaling, CAMs, citrate cycles pathways were diferentially enriched. Enriched genes like TSKU, VTG1, SGK, CDK2 etc. in these pathways might be involved in acclimation of organisms into diverse climatic conditions. The qRT‑PCR result also corroborated the RNA‑Seq fndings with R2 of 0.76, 0.80, 0.81, and 0.93 for liver, breast, caecum, and gizzard respectively. Our fndings can improve the understanding of environmental acclimation process in chicken. Recently, consumption of chicken meat has increased worldwide because of its rich nutrition, low cost, high quality protein, low cholesterol, and low fat1.
    [Show full text]
  • GC-MS Metabolomics Reveals Metabolic Differences of the Farmed
    www.nature.com/scientificreports OPEN GC-MS metabolomics reveals metabolic diferences of the farmed Mandarin fsh Siniperca chuatsi in recirculating ponds aquaculture system and pond Mingsong Xiao 1*, Kelin Qian2, Yuliang Wang1 & Fangyin Bao1 Siniperca chuatsi is currently one of the most important economic farmed freshwater fsh in China. The aim of this study was to evaluate the metabolic profle of recirculating ponds aquaculture system (RAS)- farmed S. chuatsi. Gas Chromatography-Mass Spectrophotometry (GC-MS) metabolomic platform was used to comprehensively analyze the efects of recirculating ponds aquaculture system (RAS) on the Mandarin fsh S. chuatsi metabolism. Database searching and statistical analysis revealed that there were altogether 335 metabolites quantifed (similarity > 0) and 205 metabolites were identifed by mass spectrum matching with a spectral similarity > 700. Among the 335 metabolites quantifed, 33 metabolites were signifcantly diferent (VIP > 1 and p < 0.05) between RAS and pond groups. In these thirty-three metabolites, taurine, 1-Hexadecanol, Shikimic Acid, Alloxanoic Acid and Acetaminophen were higher in the pond group, while 28 metabolites were increased notably in the RAS group. The biosynthesis of unsaturated fatty acids, lysosome, tryptophan metabolism were recommended as the KEGG pathway maps for S. chuatsi farmed in RAS. RAS can provide comprehensive benefts to the efects of Siniperca chuatsi metabolism, which suggest RAS is an efcient, economic, and environmentally friendly farming system compared to pond system. Te Chinese mandarin fsh Siniperca chuatsi (Basilewsky) is a freshwater fsh with high economic value and is endemic to East Asia, specially distributed in the Yangtze River drainage in China1. Te resources of wild S.
    [Show full text]
  • Pathview: Pathway Based Data Integration and Visualization
    Pathview: pathway based data integration and visualization Weijun Luo (luo weijun AT yahoo.com) May 19, 2021 Abstract In this vignette, we demonstrate the pathview package as a tool set for pathway based data integration and visualization. It maps and renders user data on relevant pathway graphs. All users need is to supply their gene or compound data and specify the target pathway. Pathview automatically downloads the pathway graph data, parses the data file, maps user data to the pathway, and renders pathway graph with the mapped data. Although built as a stand-alone program, pathview may seamlessly integrate with pathway and gene set (enrichment) analysis tools for a large-scale and fully automated analysis pipeline. In this vignette, we introduce common and advanced uses of pathview. We also cover package installation, data preparation, other useful features and common application errors. In gage package, vignette "RNA-Seq Data Pathway and Gene-set Analysis Workflows" demonstrates GAGE/Pathview workflows on RNA-seq (and microarray) pathway analysis. 1 Cite our work Please cite the Pathview paper formally if you use this package. This will help to support the maintenance and growth of the open source project. Weijun Luo and Cory Brouwer. Pathview: an R/Bioconductor package for pathway-based data integration and visualization. Bioinformatics, 29(14):1830-1831, 2013. doi: 10.1093/bioinformatics/btt285. 2 Quick start with demo data This is the most basic use of pathview, please check the full description below for details. Here we assume that the input data are already read in R as in the demo examples.
    [Show full text]
  • FMAP: Functional Mapping and Analysis Pipeline for Metagenomics and Metatranscriptomics Studies Jiwoong Kim1,2†, Min Soo Kim1,2†, Andrew Y
    Kim et al. BMC Bioinformatics (2016) 17:420 DOI 10.1186/s12859-016-1278-0 SOFTWARE Open Access FMAP: Functional Mapping and Analysis Pipeline for metagenomics and metatranscriptomics studies Jiwoong Kim1,2†, Min Soo Kim1,2†, Andrew Y. Koh2,4,5, Yang Xie1,2,3* and Xiaowei Zhan1,6* Abstract Background: Given the lack of a complete and comprehensive library of microbial reference genomes, determining the functional profile of diverse microbial communities is challenging. The available functional analysis pipelines lack several key features: (i) an integrated alignment tool, (ii) operon-level analysis, and (iii) the ability to process large datasets. Results: Here we introduce our open-sourced, stand-alone functional analysis pipeline for analyzing whole metagenomic and metatranscriptomic sequencing data, FMAP (Functional Mapping and Analysis Pipeline). FMAP performs alignment, gene family abundance calculations, and statistical analysis (three levels of analyses are provided: differentially-abundant genes, operons and pathways). The resulting output can be easily visualized with heatmaps and functional pathway diagrams. FMAP functional predictions are consistent with currently available functional analysis pipelines. Conclusion: FMAP is a comprehensive tool for providing functional analysis of metagenomic/metatranscriptomic sequencing data. With the added features of integrated alignment, operon-level analysis, and the ability to process large datasets, FMAP will be a valuable addition to the currently available functional analysis toolbox. We believe that this software will be of great value to the wider biology and bioinformatics communities. Background 16S rRNA sequences and gene content using whole Recent microbiome studies have revealed the complex genome shotgun (WGS) sequencing in order to identify the functional relationships between microorganisms and their functional capabilities of microbial communities.
    [Show full text]