Michael Shmoish

Genome-wide midrange transcription profiles reveal expression level relationships in human tissue specification

MOTIVATION Genes are often characterized dichotomously as either housekeeping or single-tissue specific. We conjectured that crucial functional information resides in genes with midrange profiles of expression. RESULTS To obtain such novel information genome-wide, we have determined the mRNA expression levels for one of the largest hitherto analyzed set of 62 839 probesets in 12 representative normal human tissues. Indeed, when using a newly defined graded tissue specificity index tau, valued between 0 for housekeeping genes and 1 for tissue-specific genes, genes with midrange profiles having 0.15< tau<0.85 were found to constitute >50% of all expression patterns. We developed a binary classification, indicating for every gene the I(B) tissues in which it is overly expressed, and the 12-I(B) tissues in which it shows low expression. The 85 dominant midrange patterns with I(B)=2-11 were found to be bimodally distributed, and to contribute most significantly to the definition of tissue specification dendrograms. Our analyses provide a novel route to infer expression profiles for presumed ancestral nodes in the tissue dendrogram. Such definition has uncovered an unsuspected correlation, whereby de novo enhancement and diminution of gene expression go hand in hand. These findings highlight the importance of gene suppression events, with implications to the course of tissue specification in ontogeny and phylogeny. AVAILABILITY All data and analyses are publically available at the GeneNote website, http://genecards.weizmann.ac.il/genenote/ and, GEO accession GSE803. CONTACT doron.lancet@weizmann.ac.il SUPPLEMENTARY INFORMATION Four tables available at the above site.

GeneCards Version 3: the human gene integrator

GeneCards (www.genecards.org) is a comprehensive, authoritative compendium of annotative information about human genes, widely used for nearly 15 years. Its gene-centric content is automatically mined and integrated from over 80 digital sources, resulting in a web-based deep-linked card for each of >73 000 human gene entries, encompassing the following categories: protein coding, pseudogene, RNA gene, genetic locus, cluster and uncategorized. We now introduce GeneCards Version 3, featuring a speedy and sophisticated search engine and a revamped, technologically enabling infrastructure, catering to the expanding needs of biomedical researchers. A key focus is on gene-set analyses, which leverage GeneCards’ unique wealth of combinatorial annotations. These include the GeneALaCart batch query facility, which tabulates user-selected annotations for multiple genes and GeneDecks, which identifies similar genes with shared annotations, and finds set-shared annotations by descriptor enrichment analysis. Such set-centric features address a host of applications, including microarray data analysis, cross-database annotation mapping and gene-disorder associations for drug targeting. We highlight the new Version 3 database architecture, its multi-faceted search engine, and its semi-automated quality assurance system. Data enhancements include an expanded visualization of gene expression patterns in normal and cancer tissues, an integrated alternative splicing pattern display, and augmented multi-source SNPs and pathways sections. GeneCards now provides direct links to gene-related research reagents such as antibodies, recombinant proteins, DNA clones and inhibitory RNAs and features gene-related drugs and compounds lists. We also portray the GeneCards Inferred Functionality Score annotation landscape tool for scoring a gene’s functional information status. Finally, we delineate examples of applications and collaborations that have benefited from the GeneCards suite. Database URL: www.genecards.org

Human Gene-Centric Databases at the Weizmann Institute of Science: GeneCards, UDB, CroW 21 and HORDE

Recent enhancements and current research in the GeneCards (GC) (http://bioinfo.weizmann.ac.il/cards/) project are described, including the addition of gene expression profiles and integrated gene locations. Also highlighted are the contributions of specialized associated human gene-centric databases developed at the Weizmann Institute. These include the Unified Database (UDB) (http://bioinfo.weizmann.ac.il/udb) for human genome mapping, the human Chromosome 21 database at the Weizmann Insti-tute (CroW 21) (http://bioinfo.weizmann.ac.il/crow21), and the Human Olfactory Receptor Data Explora-torium (HORDE) (http://bioinfo.weizmann.ac.il/HORDE). The synergistic relationships amongst these efforts have positively impacted the quality, quantity and usefulness of the GeneCards gene compendium.

Novel definition files for human GeneChips based on GeneAnnot

BackgroundImprovements in genome sequence annotation revealed discrepancies in the original probeset/gene assignment in Affymetrix microarray and the existence of differences between annotations and effective alignments of probes and transcription products. In the current generation of Affymetrix human GeneChips, most probesets include probes matching transcripts from more than one gene and probes which do not match any transcribed sequence.ResultsWe developed a novel set of custom Chip Definition Files (CDF) and the corresponding Bioconductor libraries for Affymetrix human GeneChips, based on the information contained in the GeneAnnot database. GeneAnnot-based CDFs are composed of unique custom-probesets, including only probes matching a single gene.ConclusionGeneAnnot-based custom CDFs solve the problem of a reliable reconstruction of expression levels and eliminate the existence of more than one probeset per gene, which often leads to discordant expression signals for the same transcript when gene differential expression is the focus of the analysis. GeneAnnot CDFs are freely distributed and fully compliant with Affymetrix standards and all available software for gene expression analysis. The CDF libraries are available from http://www.xlab.unimo.it/GA_CDF, along with supplementary information (CDF libraries, installation guidelines and R code, CDF statistics, and analysis results).

Viral photosynthetic reaction center genes and transcripts in the marine environment

Cyanobacteria of the genera Synechococcus and Prochlorococcus are important contributors to photosynthetic productivity in the open ocean. The discovery of genes (psbA, psbD) that encode key photosystem II proteins (D1, D2) in the genomes of phages that infect these cyanobacteria suggests new paradigms for the regulation, function and evolution of photosynthesis in the vast pelagic ecosystem. Reports on the prevalence and expression of phage photosynthesis genes, and evolutionary data showing a potential recombination of phage and host genes, suggest a model in which phage photosynthesis genes help support photosynthetic activity in their hosts during the infection process. Here, using metagenomic data in natural ocean samples, we show that about 60% of the psbA genes in surface water along the global ocean sampling transect are of phage origin, and that the phage genes are undergoing an independent selection for distinct D1 proteins. Furthermore, we show that different viral psbA genes are expressed in the environment.

Comparative community genomics in the Dead Sea: an increasingly extreme environment

Owing to the extreme salinity (∼10 times saltier than the oceans), near toxic magnesium levels (∼2.0 M Mg2+), the dominance of divalent cations, acidic pH (6.0) and high-absorbed radiation flux rates, the Dead Sea represents a unique and harsh ecosystem. Measures of microbial presence (microscopy, pigments and lipids) indicate that during rare bloom events after exceptionally rainy seasons, the microbial communities can reach high densities. However, most of the time, when the Dead Sea level is declining and halite is precipitating from the water column, it is difficult to reliably measure the presence of microorganisms and their activities. Although a number of halophilic Archaea have been previously isolated from the Dead Sea, polar lipid analyses of biomass collected during Dead Sea blooms suggested that these isolates were not the major components of the microbial community of these blooms. In this study, in an effort to characterize the perennial microbial community of the Dead Sea and compare it with bloom assemblages, we performed metagenomic analyses of concentrated biomass from hundreds of liters of brine and of microbial material from the last massive Dead Sea bloom. The difference between the two conditions was reflected in community composition and diversity, in which the bloom was different and less diverse from the residual brine population. The distributional patterns of microbial genes suggested Dead Sea community trends in mono- and divalent cation metabolisms as well as in transposable elements. This may indicate possible mechanisms and pathways enabling these microbes to survive in such a harsh environment.

Microbial community genomics in eastern Mediterranean Sea surface waters

Offshore waters of the eastern Mediterranean Sea are one of the most oligotrophic regions on Earth in which the primary productivity is phosphorus limited. To study the unexplored function and physiology of microbes inhabiting this system, we have analyzed a genomic library from the eastern Mediterranean Sea surface waters by sequencing both termini of nearly 5000 clones. Genome recruitment strategies showed that the majority of high-scoring pairs corresponded to genomes from the Alphaproteobacteria (SAR11-like and Rhodobacterales), Cyanobacteria (Synechococcus and high-light adapted Prochlorococcus) and diverse uncultured Gammaproteobacteria. The community structure observed, as evaluated by both protein similarity scores or metabolic potential, was similar to that found in the euphotic zone of the ALOHA station off Hawaii but very different from that of deep aphotic zones in both the Mediterranean Sea and the Pacific Ocean. In addition, a strong enrichment toward phosphate and phosphonate uptake and utilization metabolism was also observed.

Interactions between trabecular meshwork cells and lens epithelial cells: a possible mechanism in infantile aphakic glaucoma.

PURPOSE Infantile aphakic glaucoma may develop as a postoperative complication of early childhood cataract surgery. It has been associated with risk factors including surgery in early life and retained lens material; however, its cause and mechanism are poorly understood. This study focused on the potential role of retained lens material (specifically, exposed lens epithelial cells [LECs]) in undesired changes of the trabecular meshwork (TM) structure and function. METHODS Interactions between LECs and TM cells were studied by analyzing structural changes and differential gene and protein expression in TM cells cocultured with LECs. RESULTS Subjecting normal TM cells to the presence of LECs resulted in changes in their structural features (such as increase in volume and size, and decrease in cell-cell interactions), as well as in their protein expression (mainly cytoskeletal) and gene expression (such as genes related to organ and cell morphogenesis, inflammatory response, response to stimulus, ion homeostasis, and several signaling pathways). CONCLUSIONS Many of the changes observed in TM cells after exposure to LECs resemble alternations seen in primary open-angle glaucoma. This strengthens the suspected role of LECs in the development of aphakic glaucoma.

Genome-wide SNP-genotyping array to study the evolution of the human pathogen Vibrio vulnificus biotype 3.

Vibrio vulnificus is an aquatic bacterium and an important human pathogen. Strains of V. vulnificus are classified into three different biotypes. The newly emerged biotype 3 has been found to be clonal and restricted to Israel. In the family Vibrionaceae, horizontal gene transfer is the main mechanism responsible for the emergence of new pathogen groups. To better understand the evolution of the bacterium, and in particular to trace the evolution of biotype 3, we performed genome-wide SNP genotyping of 254 clinical and environmental V. vulnificus isolates with worldwide distribution recovered over a 30-year period, representing all phylogeny groups. A custom single-nucleotide polymorphism (SNP) array implemented on the Illumina GoldenGate platform was developed based on 570 SNPs randomly distributed throughout the genome. In general, the genotyping results divided the V. vulnificus species into three main phylogenetic lineages and an additional subgroup, clade B, consisting of environmental and clinical isolates from Israel. Data analysis suggested that 69% of biotype 3 SNPs are similar to SNPs from clade B, indicating that biotype 3 and clade B have a common ancestor. The rest of the biotype 3 SNPs were scattered along the biotype 3 genome, probably representing multiple chromosomal segments that may have been horizontally inserted into the clade B recipient core genome from other phylogroups or bacterial species sharing the same ecological niche. Results emphasize the continuous evolution of V. vulnificus and support the emergence of new pathogenic groups within this species as a recurrent phenomenon. Our findings contribute to a broader understanding of the evolution of this human pathogen.

GeneTide—Terra Incognita Discovery Endeavor: a new transcriptome focused member of the GeneCards/GeneNote suite of databases

GeneCards® is an automatically mined database of human genes that strives to create, along with its auxiliary databases—GeneLoc, GeneNote and GeneAnnot—the most inclusive resource of gene-centered information of the human genome. GeneTide, the Gene Terra Incognita Discovery Endeavor (http://genecards.weizmann.ac.il/genetide/), the newest addition to this family, is a transcriptome-focused database which aims to enhance GeneCards with additional expressed sequence tag (EST)-based genes. This is achieved by comprehensively mapping >85% of the ∼5.6 million human ESTs currently available at dbEST to known genes by means of data mining and integration of genomic resources including UniGene, DoTS, AceView and in-house resources. GeneTide thus creates comprehensive links between ESTs and GeneCards genes. Furthermore, groups of unassociated transcripts serve as a basis for defining novel EST-based GeneCards Candidates (EGCs). These EGCs, nearly 25 000 of which were defined in version 0.3 of GeneTide, are further annotated with various parameters, including splicing evidence and expression data extracted from the GeneNote database, to determine their validity as possible de novo genes.