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Porcine transcriptome analysis based on 97 non-normalized cDNA libraries and assembly of 1,021,891 expressed sequence tags

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GENOME BIOLOGY 2007年第4期8卷 R45-R45页

作者： Gorodkin, Jan Cirera, Susanna Hedegaard, Jakob Gilchrist, Michael J. Panitz, Frank Jorgensen, Claus Scheibye-Knudsen, Karsten Arvin, Troels Lumholdt, Steen Sawera, Milena Green, Trine Nielsen, Bente J. Havgaard, Jakob H. Rosenkilde, Carina Wang, Jun Li, Heng Li, Ruiqiang Liu, Bin Hu, Songnian Dong, Wei Li, Wei Yu, Jun Wang, Jian Staerfeldt, Hans-Henrik Wernersson, Rasmus Madsen, Lone B. Thomsen, Bo Hornshoj, Henrik Zhan Bujie Wang, Xuegang Wang, Xuefei Bolund, Lars Brunak, Soren Yang, Huanming Bendixen, Christian Fredholm, Merete Royal Vet & Agr Univ IBHV Div Genet & Bioinformat DK-1870 Frederiksberg C Denmark Danish Inst Agr Sci Dept Genet & Biotechnol DK-8830 Tjele Denmark Wellcome Trust Canc Res UK Gurdon Inst Cambridge CB2 1QN England Beijing Genom Inst Beijing 101300 Peoples R China Univ Aarhus Inst Human Genet DK-8000 Aarhus C Denmark Univ So Denmark Dept Biochem & Mol Biol DK-5230 Odense M Denmark BioCtr DTU Ctr Biol Sequence Anal DK-2800 Lyngby Denmark

Background: Knowledge of the structure of gene expression is essential for mammalian transcriptomics research. We analyzed a collection of more than one million porcine expressed sequence tags ( ESTs), of which two-thirds were generated in the Sino-Danish Pig Genome Project and one-third are from public databases. The Sino-Danish ESTs were generated from one normalized and 97 non-normalized cDNA libraries representing 35 different tissues and three developmental stages. Results: Using the Distiller package, the ESTs were assembled to roughly 48,000 contigs and 73,000 singletons, of which approximately 25% have a high confidence match to UniProt. Approximately 6,000 new porcine gene clusters were identified. Expression analysis based on the non-normalized libraries resulted in the following findings. The distribution of cluster sizes is scaling invariant. Brain and testes are among the tissues with the greatest number of different expressed genes, whereas tissues with more specialized function, such as developing liver, have fewer expressed genes. There are at least 65 high confidence housekeeping gene candidates and 876 cDNA library-specific gene candidates. We identified differential expression of genes between different tissues, in particular brain/spinal cord, and found patterns of correlation between genes that share expression in pairs of libraries. Finally, there was remarkable agreement in expression between specialized tissues according to Gene Ontology categories. Conclusion: This EST collection, the largest to date in pig, represents an essential resource for annotation, comparative genomics, assembly of the pig genome sequence, and further porcine transcription studies.

关键词： Gene Ontology cDNA Library additional data file Library Size Match Level

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POSaM: a fast, flexible, open-source, inkjet oligonucleotide synthesizer and microarrayer

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GENOME BIOLOGY 2004年第8期5卷 1-17页

作者： Lausted, C Dahl, T Warren, C King, K Smith, K Johnson, M Saleem, R Aitchison, J Hood, L Lasky, SR Inst Syst Biol Seattle WA 98103 USA

DNA arrays are valuable tools in molecular biology laboratories. Their rapid acceptance was aided by the release of plans for a pin-spotting microarrayer by researchers at Stanford. Inkjet microarraying is a flexible, complementary technique that allows the synthesis of arrays of any oligonucleotide sequences de novo. We describe here an open-source inkjet arrayer capable of rapidly producing sets of unique 9,800-feature arrays.

关键词： additional data file Propylene Carbonate Phosphoramidite Oligonucleotide Synthesis Print Head

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Independent centromere formation in a capricious, gene-free domain of chromosome 13q21 in Old World monkeys and pigs

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GENOME BIOLOGY 2006年第10期7卷 R91-R91页

作者： Cardone, Maria Francesca Alonso, Alicia Pazienza, Michele Ventura, Mario Montemurro, Gabriella Carbone, Lucia de Jong, Pieter J. Stanyon, Roscoe D'Addabbo, Pietro Archidiacono, Nicoletta She, Xinwei Eichler, Evan E. Warburton, Peter E. Rocchi, Mariano Univ Bari Dept Genet & Microbiol Bari Italy CUNY Mt Sinai Sch Med Dept Human Genet New York NY 10029 USA Childrens Hosp Oakland Res Inst Oakland CA 94609 USA Univ Florence Dept Anim Biol & Genet Leo Pardi Florence Italy Univ Washington Sch Med Dept Genome Sci Howard Hughes Med Inst Seattle WA 98195 USA

Background: Evolutionary centromere repositioning and human analphoid neocentromeres occurring in clinical cases are, very likely, two stages of the same phenomenon whose properties still remain substantially obscure. Chromosome 13 is the chromosome with the highest number of neocentromeres. We reconstructed the mammalian evolutionary history of this chromosome and characterized two human neocentromeres at 13q21, in search of information that could improve our understanding of the relationship between evolutionarily new centromeres, inactivated centromeres, and clinical neocentromeres. Results: Chromosome 13 evolution was studied, using FISH experiments, across several diverse superordinal phylogenetic clades spanning > 100 million years of evolution. The analysis revealed exceptional conservation among primates (hominoids, Old World monkeys, and New World monkeys), Carnivora (cat), Perissodactyla (horse), and Cetartiodactyla (pig). In contrast, the centromeres in both Old World monkeys and pig have apparently repositioned independently to a central location (13q21). We compared these results to the positions of two human 13q21 neocentromeres using chromatin immunoprecipitation and genomic microarrays. Conclusion: We show that a gene-desert region at 13q21 of approximately 3.9 Mb in size possesses an inherent potential to form evolutionarily new centromeres over, at least, approximately 95 million years of mammalian evolution. The striking absence of genes may represent an important property, making the region tolerant to the extensive pericentromeric reshuffling during subsequent evolution. Comparison of the pericentromeric organization of chromosome 13 in four Old World monkey species revealed many differences in sequence organization. The region contains clusters of duplicons showing peculiar features.

关键词： additional data file Segmental Duplication World Monkey Wooly Monkey Overgo Probe

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A first-draft human protein-interaction map

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GENOME BIOLOGY 2004年第9期5卷 1-9页

作者： Lehner, B Fraser, AG Wellcome Trust Sanger Inst Cambridge CB10 1SA England

Background: Protein-interaction maps are powerful tools for suggesting the cellular functions of genes. Although large-scale protein-interaction maps have been generated for several invertebrate species, projects of a similar scale have not yet been described for any mammal. Because many physical interactions are conserved between species, it should be possible to infer information about human protein interactions ( and hence protein function) using model organism protein-interaction datasets. Results: Here we describe a network of over 70,000 predicted physical interactions between around 6,200 human proteins generated using the data from lower eukaryotic protein-interaction maps. The physiological relevance of this network is supported by its ability to preferentially connect human proteins that share the same functional annotations, and we show how the network can be used to successfully predict the functions of human proteins. We find that combining interaction datasets from a single organism ( but generated using independent assays) and combining interaction datasets from two organisms ( but generated using the same assay) are both very effective ways of further improving the accuracy of protein-interaction maps. Conclusions: The complete network predicts interactions for a third of human genes, including 448 human disease genes and 1,482 genes of unknown function, and so provides a rich framework for biomedical research.

关键词： Gene Ontology additional data file Confidence Score Interaction dataset Human Disease Gene

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Comparative transcriptome analysis of embryonic and adult stem cells with extended and limited differentiation capacity

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GENOME BIOLOGY 2007年第8期8卷 R163-R163页

作者： Ulloa-Montoya, Fernando Kidder, Benjamin L. Pauwelyn, Karen A. Chase, Lucas G. Luttun, Aernout Crabbe, Annelies Geraerts, Martine Sharov, Alexei A. Piao, Yulan Ko, Minoru Sh Hu, Wei-Shou Verfaillie, Catherine M. Univ Minnesota Stem Cell Inst Minneapolis MN 55455 USA Univ Minnesota Dept Chem Engn & Mat Sci Minneapolis MN 55455 USA Katholieke Univ Leuven Stamcel Instituut B-3000 Louvain Belgium NIA Dev Genom & Aging Sect Genet Lab NIH Baltimore MD 21224 USA

Background: Recently, several populations of postnatal stem cells, such as multipotent adult progenitor cells (MAPCs), have been described that have broader differentiation ability than classical adult stem cells. Here we compare the transcriptome of pluripotent embryonic stem cells (ESCs), MAPCs, and lineage-restricted mesenchymal stem cells (MSCs) to determine their relationship. Results: Applying principal component analysis, non-negative matrix factorization and k-means clustering algorithms to the gene-expression data, we identified a unique gene-expression profile for MAPCs. Apart from the ESC-specific transcription factor Oct4 and other ESC transcripts, some of them associated with maintaining ESC pluripotency, MAPCs also express transcripts characteristic of early endoderm and mesoderm. MAPCs do not, however, express Nanog or Sox2, two other key transcription factors involved in maintaining ESC properties. This unique molecular signature was seen irrespective of the microarray platform used and was very similar for both mouse and rat MAPCs. As MSC-like cells isolated under MAPC conditions are virtually identical to MSCs, and MSCs cultured in MAPC conditions do not upregulate MAPC-expressed transcripts, the MAPC signature is cell-type specific and not merely the result of differing culture conditions. Conclusion: Multivariate analysis techniques clustered stem cells on the basis of their expressed gene profile, and the genes determining this clustering reflected the stem cells' differentiation potential in vitro. This comparative transcriptome analysis should significantly aid the isolation and culture of MAPCs and MAPC-like cells, and form the basis for studies to gain insights into genes that confer on these cells their greater developmental potency.

关键词： additional data file Inner Cell Mass Definitive Endoderm Mouse ESCs Primitive Endoderm

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Rapid, accurate, computational discovery of Rho-independent transcription terminators illuminates their relationship to DNA uptake

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GENOME BIOLOGY 2007年第2期8卷 R22-R22页

作者： Kingsford, Carleton L. Ayanbule, Kunmi Salzberg, Steven L. Univ Maryland Ctr Bioinformat & Computat Biol College Pk MD 20742 USA

Background: In many prokaryotes, transcription of DNA to RNA is terminated by a thymine-rich stretch of DNA following a hairpin loop. Detecting such Rho-independent transcription terminators can shed light on the organization of bacterial genomes and can improve genome annotation. Previous computational methods to predict Rho-independent terminators have been slow or limited in the organisms they consider. Results: We describe TransTermHP, a new computational method to rapidly and accurately detect Rho-independent transcription terminators. We predict the locations of terminators in 343 prokaryotic genomes, representing the largest collection of predictions available. In Bacillus subtilis, we can detect 93% of known terminators with a false positive rate of just 6%, comparable to the best-known methods. Outside the Firmicutes division, we find that Rho-independent termination plays a large role in the Neisseria and Vibrio genera, the Pasteurellaceae (including the Haemophilus genus) and several other species. In Neisseria and Pasteurellaceae, terminator hairpins are frequently formed by closely spaced, complementary instances of exogenous DNA uptake signal sequences. We quantify the propensity for terminators to include these sequences. In the process, we provide the first discussion of potential uptake signals in Haemophilus ducreyi and Mannheimia succiniciproducens, and we discuss the preference for a particular configuration of uptake signal sequences within terminators. Conclusion: Our new fast and accurate method for detecting transcription terminators has allowed us to identify and analyze terminators in many new genomes and to identify DNA uptake signal sequences in several species where they have not been previously reported. Our software and predictions are freely available.

关键词： additional data file Extended Motif Hairpin Stem Uptake Signal Sequence Good Terminator

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Inferring protein domain interactions from databases of interacting proteins

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GENOME BIOLOGY 2005年第10期6卷 R89-R89页

作者： Riley, R Lee, C Sabatti, C Eisenberg, D Univ Calif Los Angeles Inst Genom & Proteom Los Angeles CA 90095 USA Univ Calif Los Angeles David Geffen Sch Med UCLA Dept Human Genet Los Angeles CA 90095 USA Univ Calif Los Angeles Howard Hughes Med Inst Los Angeles CA 90095 USA

We describe domain pair exclusion analysis ( DPEA), a method for inferring domain interactions from databases of interacting proteins. DPEA features a log odds score, E-ij, reflecting confidence that domains i and j interact. We analyzed 177,233 potential domain interactions underlying 26,032 protein interactions. In total, 3,005 high-confidence domain interactions were inferred, and were evaluated using known domain interactions in the Protein data Bank. DPEA may prove useful in guiding experiment-based discovery of previously unrecognized domain interactions.

关键词： Protein data Bank additional data file Domain Interaction Domain Pair Protein Interaction data

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Identification of ciliary and ciliopathy genes in Caenorhabditis elegans through comparative genomics

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GENOME BIOLOGY 2006年第12期7卷 R126-R126页

作者： Chen, Nansheng Mah, Allan Blacque, Oliver E. Chu, Jeffrey Phgora, Kiran Bakhoum, Mathieu W. Newbury, C. Rebecca Hunt Khattra, Jaswinder Chan, Susanna Go, Anne Efimenko, Evgeni Johnsen, Robert Phirke, Prasad Swoboda, Peter Marra, Marco Moerman, Donald G. Leroux, Michel R. Baillie, David L. Stein, Lincoln D. Cold Spring Harbor Lab Cold Spring Harbor NY 11724 USA Simon Fraser Univ Dept Mol Biol & Biochem Burnaby BC V5A 1S6 Canada Univ Coll Dublin Sch Biomol & Biomed Sci Conway Inst Dublin Ireland Univ British Columbia Dept Zool Vancouver BC V6T 1Z4 Canada Sodertorn Univ Coll Sch Life Sci Karolinska Inst Dept Biosci & Nutr S-14189 Huddinge Sweden British Columbia Canc Agcy Genome Sci Ctr Vancouver BC V5Z 4S6 Canada

Background: The recent availability of genome sequences of multiple related Caenorhabditis species has made it possible to identify, using comparative genomics, similarly transcribed genes in Caenorhabditis elegans and its sister species. Taking this approach, we have identified numerous novel ciliary genes in C. elegans, some of which may be orthologs of unidentified human ciliopathy genes. Results: By screening for genes possessing canonical X-box sequences in promoters of three Caenorhabditis species, namely C. elegans, C. briggsae and C. remanei, we identified 93 genes ( including known X-box regulated genes) that encode putative components of ciliated neurons in C. elegans and are subject to the same regulatory control. For many of these genes, restricted anatomical expression in ciliated cells was confirmed, and control of transcription by the ciliogenic DAF-19 RFX transcription factor was demonstrated by comparative transcriptional profiling of different tissue types and of daf-19(+) and daf-19(-) animals. Finally, we demonstrate that the dye-filling defect of dyf-5( mn400) animals, which is indicative of compromised exposure of cilia to the environment, is caused by a nonsense mutation in the serine/threonine protein kinase gene M04C9.5. Conclusion: Our comparative genomics-based predictions may be useful for identifying genes involved in human ciliopathies, including Bardet-Biedl Syndrome ( BBS), since the C. elegans orthologs of known human BBS genes contain X-box motifs and are required for normal dye filling in C. elegans ciliated neurons.

关键词： additional data file Hide Markov Model Profile Caenorhabditis Species GeneChip Hybridization Ciliary Gene

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Meta-analysis of gene expression profiles in breast cancer: toward a unified understanding of breast cancer subtyping and prognosis signatures

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BREAST CANCER RESEARCH 2008年第4期10卷 1-11页

作者： Wirapati, Pratyaksha Sotiriou, Christos Kunkel, Susanne Farmer, Pierre Pradervand, Sylvain Haibe-Kains, Benjamin Desmedt, Christine Ignatiadis, Michail Sengstag, Thierry Schuetz, Frederic Goldstein, Darlene R. Piccart, Martine Delorenzi, Mauro Univ Libre Bruxelles Translat Res & Med Oncol Unit Inst Jules Bordet B-1000 Brussels Belgium Univ Lausanne Swiss Inst Bioinformat CH-1015 Lausanne Switzerland Swiss Inst Expt Canc Res Natl Ctr Competence Res CH-1066 Epalinges Switzerland Univ Lausanne Ctr Integrat Genom DNA Array Facil CH-1015 Lausanne Switzerland Free Univ Brussels Machine Learning Grp B-1050 Brussels Belgium Ecole Polytech Fed Lausanne Inst Math CH-1015 Lausanne Switzerland

Introduction Breast cancer subtyping and prognosis have been studied extensively by gene expression profiling, resulting in disparate signatures with little overlap in their constituent genes. Although a previous study demonstrated a prognostic concordance among gene expression signatures, it was limited to only one dataset and did not fully elucidate how the different genes were related to one another nor did it examine the contribution of well-known biological processes of breast cancer tumorigenesis to their prognostic performance. Method To address the above issues and to further validate these initial findings, we performed the largest meta-analysis of publicly available breast cancer gene expression and clinical data, which are comprised of 2,833 breast tumors. Gene coexpression modules of three key biological processes in breast cancer ( namely, proliferation, estrogen receptor [ER], and HER2 signaling) were used to dissect the role of constituent genes of nine prognostic signatures. Results Using a meta-analytical approach, we consolidated the signatures associated with ER signaling, ERBB2 amplification, and proliferation. Previously published expression-based nomenclature of breast cancer 'intrinsic' subtypes can be mapped to the three modules, namely, the ER-/HER2(-) (basal-like), the HER2(+) (HER2-like), and the low- and high-proliferation ER+/HER2(-) subtypes (luminal A and B). We showed that all nine prognostic signatures exhibited a similar prognostic performance in the entire dataset. Their prognostic abilities are due mostly to the detection of proliferation activity. Although ER- status (basal-like) and ERBB2(+) expression status correspond to bad outcome, they seem to act through elevated expression of proliferation genes and thus contain only indirect information about prognosis. Clinical variables measuring the extent of tumor progression, such as tumor size and nodal status, still add independent prognostic information to proliferation genes. Co

关键词： Breast Cancer additional data file Intrinsic Subtype Module Score Prognostic Performance

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Dynamic evolution of selenocysteine utilization in bacteria: a balance between selenoprotein loss and evolution of selenocysteine from redox active cysteine residues

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GENOME BIOLOGY 2006年第10期7卷 R94-R94页

作者： Zhang, Yan Romero, Hector Salinas, Gustavo Gladyshev, Vadim N. Univ Nebraska Dept Biochem Lincoln NE 68588 USA Fac Ciencias Inst Biol Dpto Biol Celular & Mol Lab Org & Evoluc Genoma Montevideo 11400 Uruguay Fac Ciencias Quim Inst Biol Catedra Inmunol Montevideo 11600 Uruguay

Background: Selenocysteine (Sec) is co-translationally inserted into protein in response to UGA codons. It occurs in oxidoreductase active sites and often is catalytically superior to cysteine (Cys). However, Sec is used very selectively in proteins and organisms. The wide distribution of Sec and its restricted use have not been explained. Results: We conducted comparative genomics and phylogenetic analyses to examine dynamics of Sec decoding in bacteria at both selenium utilization trait and selenoproteome levels. These searches revealed that 21.5% of sequenced bacteria utilize Sec, their selenoproteomes have 1 to 31 selenoproteins, and selenoprotein-rich organisms are mostly Deltaproteobacteria or Firmicutes/Clostridia. Evolutionary histories of selenoproteins suggest that Cys-to-Sec replacement is a general trend for most selenoproteins. In contrast, only a small number of Sec-to-Cys replacements were detected, and these were mostly restricted to formate dehydrogenase and selenophosphate synthetase families. In addition, specific selenoprotein gene losses were observed in many sister genomes. Thus, the Sec/Cys replacements were mostly unidirectional, and increased utilization of Sec by existing protein families was counterbalanced by loss of selenoprotein genes or entire selenoproteomes. Lateral transfers of the Sec trait were an additional factor, and we describe the first example of selenoprotein gene transfer between archaea and bacteria. Finally, oxygen requirement and optimal growth temperature were identified as environmental factors that correlate with changes in Sec utilization. Conclusion: Our data reveal a dynamic balance between selenoprotein origin and loss, and may account for the discrepancy between catalytic advantages provided by Sec and the observed low number of selenoprotein families and Sec-utilizing organisms.

关键词： Selenium Horizontal Gene Transfer additional data file Horizontal Gene Transfer Event SECIS Element

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