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PDStat : Statistical approach to protein domain frequency in various tissues and tumor
Mina Jeon,Jungrye Nam,Jae young Han,Heebal Kim 한국가금학회 2005 한국가금학회 정기총회 및 학술발표회 Vol.22 No.-
Protein domain은 단백질의 구조적, 기능적, 진화적 단위로 domain 빈도에 대한 분석을 통해 특정 유전자 그룹에 대한 특성 규명이 가능하다. 여기서는 Tigr TC sequence를 tumor 및 tissue 조직별로 분류하여 나타나는 domain의 빈도를 Zipf's law, Fisher exact test, bootstrapping과 같은 통계적 방법을 이용하여 분석함으로써 tumor 및 tissue 조직별 특이적인 domain을 찾고자 하였다. 그 결과 NIC, DUF890, TLE_N과 같은 tumor specific protein domain들을 규명할 수 있었다. Protein domains are the structural, functional and evolutionary units of proteins. A protein can be regarded as a sequence of its domains. Counting protein domain in a set of data, although it is a low level representation and classification, reveals a fundamental characteristic of the data.
Metagenome Analysis of Protein Domain Collocation within Cellulase Genes of Goat Rumen Microbes
Lim, SooYeon,Seo, Jaehyun,Choi, Hyunbong,Yoon, Duhak,Nam, Jungrye,Kim, Heebal,Cho, Seoae,Chang, Jongsoo Asian Australasian Association of Animal Productio 2013 Animal Bioscience Vol.26 No.8
In this study, protein domains with cellulase activity in goat rumen microbes were investigated using metagenomic and bioinformatic analyses. After the complete genome of goat rumen microbes was obtained using a shotgun sequencing method, 217,892,109 pair reads were filtered, including only those with 70% identity, 100-bp matches, and thresholds below $E^{-10}$ using METAIDBA. These filtered contigs were assembled and annotated using blastN against the NCBI nucleotide database. As a result, a microbial community structure with 1431 species was analyzed, among which Prevotella ruminicola 23 bacteria and Butyrivibrio proteoclasticus B316 were the dominant groups. In parallel, 201 sequences related with cellulase activities (EC.3.2.1.4) were obtained through blast searches using the enzyme.dat file provided by the NCBI database. After translating the nucleotide sequence into a protein sequence using Interproscan, 28 protein domains with cellulase activity were identified using the HMMER package with threshold E values below $10^{-5}$. Cellulase activity protein domain profiling showed that the major protein domains such as lipase GDSL, cellulase, and Glyco hydro 10 were present in bacterial species with strong cellulase activities. Furthermore, correlation plots clearly displayed the strong positive correlation between some protein domain groups, which was indicative of microbial adaption in the goat rumen based on feeding habits. This is the first metagenomic analysis of cellulase activity protein domains using bioinformatics from the goat rumen.
ChickGCE: A novel germ cell EST database for studying the early developmental stage in chickens
Kim, Heebal,Lim, Dajeong,Han, Beom Ku,Sung, Samsun,Jeon, Mina,Moon, Sunjin,Kang, Yeonkyung,Nam, Jungrye,Han, Jae Yong Elsevier 2006 Genomics Vol.88 No.2
<P><B>Abstract</B></P><P>We established a database to study germ cells during the early developmental stage in the chicken. The ChickGCE database provides integrated expressed sequence tag (EST) data from chicken testis, ovary, embryonic gonads, and primordial germ cells. We gathered data on 10,294 ESTs from approximately 1000 embryonic gonads, and we experimentally determined 10,851 ESTs from primordial germ cells purified from 7955 embryonic gonads by magnetically activated cell sorting. The EST testis and ovary datasets were retrieved from the public database of The Institute for Genomic Research (TIGR). The EST data were clustered and assembled into unique sequences, contigs, and singletons. The ChickGCE database provides functional annotation, identification, and putative embryonic germ-cell-specific novel transcripts based on the Gene Ontology database, as well as statistical analyses of expression patterns and pair-wise comparisons of two types of tissue- and germ-cell-specific alternative splicing events in the chicken. The new database is accessible online and queries can be answered using several search options, including tissue database searches, keywords, clone IDs, expected values, and BLAST search scores.</P>