Editorial Functional Genomics, Genetics, and Bioinformaticsdownloads.hindawi.com › journals › bmri › 2015 › 184824.pdf · Functional Genomics, Genetics, and Bioinformatics

EditorialFunctional Genomics Genetics and Bioinformatics

Youping Deng1 Hongwei Wang2 Ryuji Hamamoto2 David Schaffer3 and Shiwei Duan4

1Department of Internal Medicine Rush University Cancer Center Rush University Medical Center Chicago IL 60612 USA2Department of Medicine University of Chicago Chicago IL 60637 USA3Department of Bioengineering Binghamton University Binghamton NY 13902 USA4School of Medicine Ningbo University Ningbo Zhejiang 315211 China

Correspondence should be addressed to Youping Deng youping dengrushedu

Received 10 December 2014 Accepted 10 December 2014

Copyright copy 2015 Youping Deng et al This is an open access article distributed under the Creative Commons Attribution Licensewhich permits unrestricted use distribution and reproduction in any medium provided the original work is properly cited

Biology has become the land of the ldquo-omicsrdquo including geno-mics [1] transcriptomics [2 3] epigenomics [4] proteomics[5] lipidomics [6 7] and metabolomics [8] Each of theseldquo-omicsrdquo generates a huge amount of high-throughput dataand it is a challenge both to analyze these data and to furtherinvestigate the function of specific molecules Though moregenomes have been completed due to the rapid developmentof sequencing technology [9] we cannot understand the info-rmation contained within a genome until we mine out itsimplicated functions including downstream transcriptiontranslation epigeneticsmodulation andmetabolic pathwaysIn this special issue we mainly focus on functional ldquo-omicsrdquoand bioinformatics

The Peer-reviewed papers are collected in the specialissue They are approximately divided into three areas bioin-formatics functional genomics and functional genetics Themajority of the papers are purely bioinformatics relatedpapers We define bioinformatics papers as those using com-putational tools or developing methods to analyze functionalldquo-omicsrdquo data without using wet labs Two papers fell into thecategory of functional gen-omics which is focused on usingwhole genome level wet-lab technology to find importantmolecules and investigate their potential functions Fivepapers are considered as functional genetics papers Func-tional genetics is a broad concept here and these papers areconcentrated on studying themolecular functions andmech-anisms of individual molecules using wet-lab experimentalapproaches

Bioinformatics In the bioinformatics papers four papers dealwith transcriptomics data F Wang et al developed a novelapproach for coexpression analysis of E2F1-3 andMYC targetgenes in chronic myelogenous leukemia (CML) they founda significant difference in the coexpression patterns of thosecandidate target genes between the normal and the CMLgroups It is challenging to analyze the quantity of imagedata on gene expression A Shlemov et al developed amethod called 2D singular spectrum analysis (2D-SSA) forapplication to 2D and 3D datasets of embryo images relatedto gene expression it turned out to work pretty well J Liet al characterized putative cis-regulatory elements (CREs)associated withmalemeiocyte-expressed genes using in silicotools They found that the upstream regions (1 kb) of the top50 genes preferentially expressed in Arabidopsis meiocytespossessed conserved motifs which were potential bindingsites of transcription factors NAGNAG alternative splicingplays an important role in biological processes and representsa highly adaptable system for posttranslational regulation ofgene function Interestingly X Sun et al identified about 31NAGNAG alternative splicing sites that were identified inhuman large intergenic noncoding RNAs (lincRNAs)

Three papers are focused on the deification of new genefamily members and gene evolution Conotoxins are smalldisulfide-rich neurotoxic peptides which can bind to ionchannels with very high specificity and regulate their activ-ities H Ding et al developed a novel method called iCTX-Type which is a sequence-based predictor that can be used to

Hindawi Publishing CorporationBioMed Research InternationalVolume 2015 Article ID 184824 3 pageshttpdxdoiorg1011552015184824

2 BioMed Research International

identify the types of conotoxins in targeting ion channels Auser-friendly web tool is also available Y-Z Zhou et al ana-lyzed the evolution pattern and function diversity of PPARgene family members based on 63 homology sequences ofPPARgenes from31 speciesThey found that gene duplicationevents selection pressures onHOLI domain and the variantson promoter and 31015840UTR are critical for PPARs evolutionand acquiring diversity functions There has recently beenconsiderable focus on its two human pathogenic species Nmeningitidis andN gonorrhoeae which belong toNeisseria agenus of gram-negative bacteria D Yu et al selected 18 Neis-seria genomes preformed a comparative genome analysisand identified 635 genes with recombination signals and 10genes that showed significant evidence of positive selectionFurther functional analyses revealed that no functional biaswas found in the recombined genes The data help us tounderstand the adaptive evolution in Neisseria

One paper tried to solve the key algorithm issue calledthe all-pairs suffix-prefix matching problem which is crucialfor de novo genome assembly M H Rachid et al developeda space-economical solution to the problem using the gen-eralized Sadakane compressed suffix tree One paper con-ducted a comparative genomics analysis R Cecagno et alfound that the versatile gene repertoire in the genome ofrhizosphere bacterium Azospirillum amazonense could havebeen acquired from distantly related bacteria from horizontaltransfer They also demonstrated that the coding sequencerelated to production of phytohormones such as flavinmonooxygenase and aldehyde oxidase is likely to representthe tryptophan-dependent TAM pathway for auxin produc-tion in this bacterium They conclude that the genomicstructure of the bacteria has evolved to meet the requirementfor adaptation to the rhizosphere and interaction with hostplants

One article conducted a meta-analysis H Ye et al havedemonstrated that rs2228671 is a protective factor of CHD inEuropeans One paper is concentrated on the microorganismbioinformatics Y Ding et al recognized the roles of the syn-onymous codon usage in the formation of nsp1120572 structure ofporcine reproductive and respiratory syndrome virus PRRSV

Functional Genomics There are two papers that conductedgene association studies based on genome wide data J Li etal found that the presence of ATT1205764haplotype was associatedwith an increased risk of mental retardation (MR) in childrenbut did not find any significant association between singleloci of the four common ApoE polymorphisms (minus491ATminus427TC minus219TG and 120576234) and MR or borderline MRJ Zhou et al did not find an association between rs7529229and chronic heart disease (CHD) in Han Chinese Howevertheir meta-analyses indicated that rs7529229 was associatedwith the CHD risk in Europeans

Functional Genetics There are 5 articles that investigate theindividual gene function in different areas Two papers arerelated to neural diseases G-M Chang et al found thatactivating NF-120581B signaling pathway can protect intestinalepithelial cell No 6 against fission neutron irradiation X-SLiu et al demonstrated that hepatocyte growth factor (HGF)

could promote the regeneration of damaged Parkinsonrsquos dis-ease (PD) cells at higher efficacy than the supernatant fromhUC-MSCs alone Thus the combination of hUC-MSC withHGF could potentially be a new biological treatment forPD One paper is focused on cancer N Ji et al found thatcelastrol had antiprostate cancer effects partially through thedownregulation of the expression level of hERG channel inDU145 cells suggesting that celastrolmay be a potential agentagainst prostate cancer with a mechanism of blocking thehERG channel One paper is studying heart disease Z Luet al reported that the levels of NT-proBNP and CCR wereclosely related to the occurrence of HF and were independentrisk factors for heart failure (HF) Meanwhile there was asignificant negative correlation between the levels of NT-proBNP and CCR One interesting paper is trying to under-stand the function of Japanese encephalitis virus (JEV) andthey have demonstrated that RNA recombination in JEVoccurs unequally in different cell types They conclude thatthe adjustment of viral RNA to an appropriately lower level inmosquito cells prevents overgrowth of the virus and is benefi-cial for cells to survive the infection

In summary this special issue presents a broad range oftopics from functional genomics genetics and bioinformat-ics It covers a variety of diseases such as cancer heart andneural and infectious diseases The study organisms includehuman mouse plant andmicroorganismsWe hope that thereaders will find interesting knowledge and methods in theissue

Youping DengHongwei Wang

Ryuji HamamotoDavid SchafferShiwei Duan

References

[1] M Jia Y Liu Z Shen et al ldquoHDAM a resource of humandisease associated mutations from next generation sequencingstudiesrdquo BMC Medical Genomics vol 6 supplement 1 articleS16 2013

[2] Y Deng S A Meyer X Guan et al ldquoAnalysis of common andspecific mechanisms of liver function affected by nitrotoluenecompoundsrdquo PLoS ONE vol 6 no 2 Article ID e14662 2011

[3] H Jiang Y Deng H-S Chen et al ldquoJoint analysis of two micr-oarray gene-expression data sets to select lung adenocarcinomamarker genesrdquo BMC Bioinformatics vol 5 article 81 2004

[4] J Melson Y Li E Cassinotti et al ldquoCommonality and differ-ences of methylation signatures in the plasma of patients withpancreatic cancer and colorectal cancerrdquo International Journalof Cancer vol 134 no 11 pp 2656ndash2662 2014

[5] F Xu G Li C Zhao et al ldquoGlobal protein interactome explo-ration through mining genome-scale data in Arabidopsis tha-lianardquo BMC Genomics vol 11 article S2 supplement 2 2010

[6] Y Wang C Zhao J Mao et al ldquoIntegrated lipidomics andtranscriptomic analysis of peripheral blood reveals significantlyenriched pathways in type 2 diabetes mellitusrdquo BMC MedicalGenomics vol 6 no 1 article S12 2013

BioMed Research International 3

[7] X Zhou J Mao J Ai et al ldquoIdentification of plasma lipidbiomarkers for prostate cancer by lipidomics and bioinformat-icsrdquo PLoS ONE vol 7 no 11 Article ID e48889 2012

[8] T W-M Fan A N Lane and R M Higashi ldquoThe promise ofmetabolomics in cancer molecular therapeuticsrdquoCurrent Opin-ion in Molecular Therapeutics vol 6 no 6 pp 584ndash592 2004

[9] FWang L Lu C Yu et al ldquoDevelopment of a novel DNA sequ-encingmethodnot only for hepatitis B virus genotyping but alsofor drug resistant mutation detectionrdquo BMCMedical Genomicsvol 6 no 1 article S15 2013

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2 BioMed Research International

identify the types of conotoxins in targeting ion channels Auser-friendly web tool is also available Y-Z Zhou et al ana-lyzed the evolution pattern and function diversity of PPARgene family members based on 63 homology sequences ofPPARgenes from31 speciesThey found that gene duplicationevents selection pressures onHOLI domain and the variantson promoter and 31015840UTR are critical for PPARs evolutionand acquiring diversity functions There has recently beenconsiderable focus on its two human pathogenic species Nmeningitidis andN gonorrhoeae which belong toNeisseria agenus of gram-negative bacteria D Yu et al selected 18 Neis-seria genomes preformed a comparative genome analysisand identified 635 genes with recombination signals and 10genes that showed significant evidence of positive selectionFurther functional analyses revealed that no functional biaswas found in the recombined genes The data help us tounderstand the adaptive evolution in Neisseria

One paper tried to solve the key algorithm issue calledthe all-pairs suffix-prefix matching problem which is crucialfor de novo genome assembly M H Rachid et al developeda space-economical solution to the problem using the gen-eralized Sadakane compressed suffix tree One paper con-ducted a comparative genomics analysis R Cecagno et alfound that the versatile gene repertoire in the genome ofrhizosphere bacterium Azospirillum amazonense could havebeen acquired from distantly related bacteria from horizontaltransfer They also demonstrated that the coding sequencerelated to production of phytohormones such as flavinmonooxygenase and aldehyde oxidase is likely to representthe tryptophan-dependent TAM pathway for auxin produc-tion in this bacterium They conclude that the genomicstructure of the bacteria has evolved to meet the requirementfor adaptation to the rhizosphere and interaction with hostplants

One article conducted a meta-analysis H Ye et al havedemonstrated that rs2228671 is a protective factor of CHD inEuropeans One paper is concentrated on the microorganismbioinformatics Y Ding et al recognized the roles of the syn-onymous codon usage in the formation of nsp1120572 structure ofporcine reproductive and respiratory syndrome virus PRRSV

Functional Genomics There are two papers that conductedgene association studies based on genome wide data J Li etal found that the presence of ATT1205764haplotype was associatedwith an increased risk of mental retardation (MR) in childrenbut did not find any significant association between singleloci of the four common ApoE polymorphisms (minus491ATminus427TC minus219TG and 120576234) and MR or borderline MRJ Zhou et al did not find an association between rs7529229and chronic heart disease (CHD) in Han Chinese Howevertheir meta-analyses indicated that rs7529229 was associatedwith the CHD risk in Europeans

Functional Genetics There are 5 articles that investigate theindividual gene function in different areas Two papers arerelated to neural diseases G-M Chang et al found thatactivating NF-120581B signaling pathway can protect intestinalepithelial cell No 6 against fission neutron irradiation X-SLiu et al demonstrated that hepatocyte growth factor (HGF)

could promote the regeneration of damaged Parkinsonrsquos dis-ease (PD) cells at higher efficacy than the supernatant fromhUC-MSCs alone Thus the combination of hUC-MSC withHGF could potentially be a new biological treatment forPD One paper is focused on cancer N Ji et al found thatcelastrol had antiprostate cancer effects partially through thedownregulation of the expression level of hERG channel inDU145 cells suggesting that celastrolmay be a potential agentagainst prostate cancer with a mechanism of blocking thehERG channel One paper is studying heart disease Z Luet al reported that the levels of NT-proBNP and CCR wereclosely related to the occurrence of HF and were independentrisk factors for heart failure (HF) Meanwhile there was asignificant negative correlation between the levels of NT-proBNP and CCR One interesting paper is trying to under-stand the function of Japanese encephalitis virus (JEV) andthey have demonstrated that RNA recombination in JEVoccurs unequally in different cell types They conclude thatthe adjustment of viral RNA to an appropriately lower level inmosquito cells prevents overgrowth of the virus and is benefi-cial for cells to survive the infection

In summary this special issue presents a broad range oftopics from functional genomics genetics and bioinformat-ics It covers a variety of diseases such as cancer heart andneural and infectious diseases The study organisms includehuman mouse plant andmicroorganismsWe hope that thereaders will find interesting knowledge and methods in theissue

Youping DengHongwei Wang

Ryuji HamamotoDavid SchafferShiwei Duan

References

[1] M Jia Y Liu Z Shen et al ldquoHDAM a resource of humandisease associated mutations from next generation sequencingstudiesrdquo BMC Medical Genomics vol 6 supplement 1 articleS16 2013

[2] Y Deng S A Meyer X Guan et al ldquoAnalysis of common andspecific mechanisms of liver function affected by nitrotoluenecompoundsrdquo PLoS ONE vol 6 no 2 Article ID e14662 2011

[3] H Jiang Y Deng H-S Chen et al ldquoJoint analysis of two micr-oarray gene-expression data sets to select lung adenocarcinomamarker genesrdquo BMC Bioinformatics vol 5 article 81 2004

[4] J Melson Y Li E Cassinotti et al ldquoCommonality and differ-ences of methylation signatures in the plasma of patients withpancreatic cancer and colorectal cancerrdquo International Journalof Cancer vol 134 no 11 pp 2656ndash2662 2014

[5] F Xu G Li C Zhao et al ldquoGlobal protein interactome explo-ration through mining genome-scale data in Arabidopsis tha-lianardquo BMC Genomics vol 11 article S2 supplement 2 2010

[6] Y Wang C Zhao J Mao et al ldquoIntegrated lipidomics andtranscriptomic analysis of peripheral blood reveals significantlyenriched pathways in type 2 diabetes mellitusrdquo BMC MedicalGenomics vol 6 no 1 article S12 2013












Volume 2014

Zoology






















Advances in

Virolog y



Volume 2014




Enzyme Research



Microbiology












Volume 2014

Zoology






















Advances in

Virolog y



Volume 2014




Enzyme Research



Microbiology








Volume 2014

Zoology






















Advances in

Virolog y



Volume 2014




Enzyme Research



Microbiology

Documents

Editorial Functional Genomics, Genetics, and Bioinformaticsdownloads.hindawi.com › journals › bmri › 2015 › 184824.pdf · Functional Genomics, Genetics, and Bioinformatics