A Pathway Analysis Tool for Analyzing Microarray Data of Species with Low Physiological Information

Pathway information provides insight into the biological processes underlying microarray data. Pathway information is widely available for humans and laboratory animals in databases through the internet, but less for other species, for example, livestock. Many software packages use species-specific gene IDs that cannot handle genomics data from other species. We developed a species-independent method to search pathways databases to analyse microarray data. Three PERL scripts were developed that use the names of the genes on the microarray. (1) Add synonyms of gene names by searching the Gene Ontology (GO) database. (2) Search the Kyoto Encyclopaedia of Genes and Genomes (KEGG) database for pathway information using this GO-enriched gene list. (3) Combine the pathway data with the microarray data and visualize the results using color codes indicating regulation. To demonstrate the power of the method, we used a previously reported chicken microarray experiment investigating line-specific reactions to Salmonella infection as an example.

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First Report of Chlamydia abortus in Farmed Fur Animals

BioMed Research International ◽

10.1155/2018/4289648 ◽

2018 ◽

Vol 2018 ◽

pp. 1-6 ◽

Cited By ~ 5

Author(s):

Zhaocai Li ◽

Ping Liu ◽

Xiaoan Cao ◽

Zhongzi Lou ◽

Kinga Zaręba-Marchewka ◽

...

Keyword(s):

Economic Loss ◽

23S Rrna ◽

Specific Gene ◽

First Report ◽

Veterinary Importance ◽

Potential Risks ◽

Species Specific ◽

Fur Animals ◽

Globally Distributed ◽

Raccoon Dogs

Chlamydia (C.) abortus, a globally distributed obligate intracellular bacterium, has attracted increasing interest according to its veterinary importance and zoonotic nature. C. abortus can infect a variety of animals and cause foetal loss in livestock resulting in economic loss. In this study, the samples collected from two farms of foxes (n=20), raccoon dogs (n=15) and minks (n=20), were investigated by Chlamydiaceae- and Chlamydia species-specific real-time PCR. The results showed that all the tested foxes (20/20) and raccoon dogs (15/15) harbored Chlamydia spp., while 5% of minks (1/20) were positive for Chlamydia spp. C. abortus was identified in all positive samples as the dominant Chlamydia species, with C. pecorum DNA coexistence in some of the rectal samples (7/20) taken from foxes. Phylogenetic analysis based on specific gene fragments of 16S rRNA, IGS-23S rRNA, and ompA revealed that all sequences obtained in this study were assigned to the Chlamydiaceae family with high similarity to C. abortus S26/3 and B577 previously identified in ruminants. This is the first report confirming that farmed foxes, raccoon dogs, and minks carry C. abortus. Further studies are needed to fully elucidate the epidemiology and pathogenicity of this pathogen in farmed fur animals as well as the potential risks to public health.

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Serological differentiation of the Ascochyta species on peas

Canadian Journal of Microbiology ◽

10.1139/m68-071 ◽

1968 ◽

Vol 14 (4) ◽

pp. 449-451 ◽

Cited By ~ 7

Author(s):

C. Madhosingh ◽

V. R. Wallen

Keyword(s):

Immune Serum ◽

Complex Pattern ◽

Serological Relationship ◽

Agar Gel ◽

Ascochyta Pinodes ◽

Ascochyta Pisi ◽

Precipitation Reactions ◽

Species Specific ◽

Specific Reactions

Specific immune serum against Ascochyta pisi was developed and three species-specific reactions were obtained by standard absorption techniques using extracts of both Ascochyta pinodella and Ascochyta pinodes. Ouchterlony tests showed a complex pattern of precipitation reactions in agar gel between the antigens from the three species and antisera developed in response to them and indicated distinct serological relationships among the three fungi. The pattern of reciprocal precipitin reactions indicates a closer serological relationship between A. pinodella and A. pinodes than between either of these two species and A. pisi. Two serologically similar antigenic components were present in the extracts from the three species.

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Profile of a mammalian sperm receptor

Development ◽

10.1242/dev.108.1.1 ◽

1990 ◽

Vol 108 (1) ◽

pp. 1-17 ◽

Cited By ~ 2

Author(s):

P.M. Wassarman

Keyword(s):

Gene Expression ◽

Zona Pellucida ◽

Specific Gene ◽

Mammalian Development ◽

Unique Nature ◽

Mammalian Fertilization ◽

Species Specific ◽

Available Information ◽

Mammalian Eggs ◽

Sperm Receptor

Complementary molecules on the surface of eggs and sperm are responsible for species-specific interactions between gametes during fertilization in both plants and animals. In this essay, several aspects of current research on the mouse egg receptor for sperm, a zona pellucida glycoprotein called ZP3, are addressed. These include the structure, synthesis, and functions of the sperm receptor during oogenesis and fertilization in mice. Several conclusions are drawn from available information. These include (I) ZP3 is a member of a unique class of glycoproteins found exclusively in the extracellular coat (zona pellucida) of mammalian eggs. (II) ZP3 gene expression is an example of oocyte-specific and, therefore, sex-specific gene expression during mammalian development. (III) ZP3 is a structural glycoprotein involved in assembly of the egg extracellular coat during mammalian oogenesis. (IV) ZP3 is a sperm receptor involved in carbohydrate-mediated gamete recognition and adhesion during mammalian fertilization. (V) ZP3 is an inducer of sperm exocytosis (acrosome reaction) during mammalian fertilization. (VI) ZP3 participates in the secondary block to polyspermy following fertilization in mammals. (VII) The extracellular coat of other mammalian eggs contains a glycoprotein that is functionally analogous to mouse ZP3. The unique nature, highly restricted expression, and multiple roles of ZP3 during mammalian development make this glycoprotein a particularly attractive subject for investigation at both the cellular and molecular levels.

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TriPOINT: a software tool to prioritize important genes in pathways and their non-coding regulators

Bioinformatics ◽

10.1093/bioinformatics/bty998 ◽

2018 ◽

Vol 35 (15) ◽

pp. 2686-2689

Author(s):

Asa Thibodeau ◽

Dong-Guk Shin

Keyword(s):

Gene Expression ◽

Software Tool ◽

Supplementary Information ◽

Analysis Tool ◽

Graph Representations ◽

Expression Levels ◽

Conducting Pathway ◽

Pathway Analysis Tool ◽

Pathway Analyses ◽

Gene Expression Levels

Abstract Summary Current approaches for pathway analyses focus on representing gene expression levels on graph representations of pathways and conducting pathway enrichment among differentially expressed genes. However, gene expression levels by themselves do not reflect the overall picture as non-coding factors play an important role to regulate gene expression. To incorporate these non-coding factors into pathway analyses and to systematically prioritize genes in a pathway we introduce a new software: Triangulation of Perturbation Origins and Identification of Non-Coding Targets. Triangulation of Perturbation Origins and Identification of Non-Coding Targets is a pathway analysis tool, implemented in Java that identifies the significance of a gene under a condition (e.g. a disease phenotype) by studying graph representations of pathways, analyzing upstream and downstream gene interactions and integrating non-coding regions that may be regulating gene expression levels. Availability and implementation The TriPOINT open source software is freely available at https://github.uconn.edu/ajt06004/TriPOINT under the GPL v3.0 license. Supplementary information Supplementary data are available at Bioinformatics online.

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RealSpot: software validating results from DNA microarray data analysis with spot images

Physiological Genomics ◽

10.1152/physiolgenomics.00236.2004 ◽

2005 ◽

Vol 21 (2) ◽

pp. 284-291 ◽

Cited By ~ 15

Author(s):

Zhongming Chen ◽

Lin Liu

Keyword(s):

Data Analysis ◽

Dna Microarray ◽

Microarray Data ◽

Microarray Experiment ◽

Current Data ◽

Microarray Data Analysis ◽

Quality Analysis ◽

Biological Knowledge ◽

Data Validation ◽

Spot Quality

The spot images from DNA microarray highly affect the discovery of biological knowledge from gene expression data. However, results from quality analysis, normalization, differential expression, and cluster analysis are rarely validated with spot images in current data analysis methods or software packages. We designed RealSpot, a software package, to validate the results by directly associating spot quality and data with spot images in a spreadsheet table. RealSpot splits hybridization images into individual spots stored in a spreadsheet table. It subsequently associates microarray data with spot images and performs data validation through the standard table operation such as sorting, searching, and editing. RealSpot has several built-in functions to facilitate data validation, including spot quality analysis, data organization, one-way ANOVA, gene ontology association, verification, import, and export. We used RealSpot to evaluate 77 slides (30,000 features each) from real hybridization experiments and to validate results from each step of data analysis. It took ∼10 min to validate results of spot quality after initial evaluation and correct ∼0.3% of falsely assigned qualities of 10,000 spots. We validated 1,641 of 2,110 differentially expressed genes identified by SAM analysis in ∼1/2 h by comparing each gene with its respective spot image. Furthermore, we found that 6 of 48 genes in one cluster from k-mean clustering method showed inconsistent trends of spot images. RealSpot is efficient for validating microarray results and thus helpful for improving the reliability of the whole microarray experiment for experimentalists.

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Comparative functional genomic analysis of Alzheimer’s affected and naturally aging brains

PeerJ ◽

10.7717/peerj.8682 ◽

2020 ◽

Vol 8 ◽

pp. e8682

Author(s):

Yi-Shian Peng ◽

Chia-Wei Tang ◽

Yi-Yun Peng ◽

Hung Chang ◽

Chien-Lung Chen ◽

...

Keyword(s):

Gene Expression ◽

Differentially Expressed Genes ◽

Microarray Data ◽

Gene List ◽

Amyloid Β ◽

Differentially Expressed ◽

Gene Expression Microarray ◽

Expression Microarray ◽

Functional Genomic Analysis ◽

Gene Expression Microarray Data

Background Alzheimer’s disease (AD) is a prevalent progressive neurodegenerative human disease whose cause remains unclear. Numerous initially highly hopeful anti-AD drugs based on the amyloid-β (Aβ) hypothesis of AD have failed recent late-phase tests. Natural aging (AG) is a high-risk factor for AD. Here, we aim to gain insights in AD that may lead to its novel therapeutic treatment through conducting meta-analyses of gene expression microarray data from AG and AD-affected brain. Methods Five sets of gene expression microarray data from different regions of AD (hereafter, ALZ when referring to data)-affected brain, and one set from AG, were analyzed by means of the application of the methods of differentially expressed genes and differentially co-expressed gene pairs for the identification of putatively disrupted biological pathways and associated abnormal molecular contents. Results Brain-region specificity among ALZ cases and AG-ALZ differences in gene expression and in KEGG pathway disruption were identified. Strong heterogeneity in AD signatures among the five brain regions was observed: HC/PC/SFG showed clear and pronounced AD signatures, MTG moderately so, and EC showed essentially none. There were stark differences between ALZ and AG. OXPHOS and Proteasome were the most disrupted pathways in HC/PC/SFG, while AG showed no OXPHOS disruption and relatively weak Proteasome disruption in AG. Metabolic related pathways including TCA cycle and Pyruvate metabolism were disrupted in ALZ but not in AG. Three pathogenic infection related pathways were disrupted in ALZ. Many cancer and signaling related pathways were shown to be disrupted AG but far less so in ALZ, and not at all in HC. We identified 54 “ALZ-only” differentially expressed genes, all down-regulated and which, when used to augment the gene list of the KEGG AD pathway, made it significantly more AD-specific.

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Single-cell RNA sequencing of Plasmodium vivax sporozoites reveals stage- and species-specific transcriptomic signatures

10.1101/2021.11.24.469176 ◽

2021 ◽

Author(s):

Anthony A Ruberto ◽

Caitlin Bourke ◽

Amélie Vantaux ◽

Steven P Maher ◽

Aaron Jex ◽

...

Keyword(s):

Single Cell ◽

Salivary Glands ◽

Plasmodium Vivax ◽

Translational Regulation ◽

Developmental Trajectory ◽

Specific Gene ◽

Developmental States ◽

Usage Patterns ◽

Gene Usage ◽

Species Specific

Plasmodium vivax sporozoites reside in the salivary glands of a mosquito before infecting a human host. Previous transcriptome-wide studies in populations of these forms were limited in their ability to elucidate cell-to-cell variation, thereby masking cellular states potentially important in understanding transmission outcomes. In this study, we performed transcription profiling on 9,947 P. vivax sporozoites to assess the extent to which they differ at single-cell resolution. We show that sporozoites residing in the mosquito's salivary glands exist in distinct developmental states, as defined by their transcriptomic signatures. Additionally, relative to P. falciparum, P. vivax displays overlapping and unique gene usage patterns, highlighting conserved and species-specific gene programs. Notably, distinguishing P. vivax from P. falciparum were a subset of P. vivax sporozoites expressing genes associated with translational regulation and repression. Finally, our comparison of single-cell transcriptomic data from P. vivax sporozoite and erythrocytic forms reveals gene usage patterns unique to sporozoites. In defining the transcriptomic signatures of individual P. vivax sporozoites, our work provides new insights into the factors driving their developmental trajectory and lays the groundwork for a more comprehensive P. vivax cell atlas.

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Genome-scale metabolic network reconstruction of model animals as a platform for translational research

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.2102344118 ◽

2021 ◽

Vol 118 (30) ◽

pp. e2102344118

Author(s):

Hao Wang ◽

Jonathan L. Robinson ◽

Pinar Kocabas ◽

Johan Gustafsson ◽

Mihail Anton ◽

...

Keyword(s):

Transgenic Mice ◽

Metabolic Network ◽

Model Organisms ◽

Protein Overexpression ◽

Sequencing Data ◽

Proteomics Data ◽

Gm2 Ganglioside ◽

Species Specific ◽

Specific Reactions ◽

Genome Scale

Genome-scale metabolic models (GEMs) are used extensively for analysis of mechanisms underlying human diseases and metabolic malfunctions. However, the lack of comprehensive and high-quality GEMs for model organisms restricts translational utilization of omics data accumulating from the use of various disease models. Here we present a unified platform of GEMs that covers five major model animals, including Mouse1 (Mus musculus), Rat1 (Rattus norvegicus), Zebrafish1 (Danio rerio), Fruitfly1 (Drosophila melanogaster), and Worm1 (Caenorhabditis elegans). These GEMs represent the most comprehensive coverage of the metabolic network by considering both orthology-based pathways and species-specific reactions. All GEMs can be interactively queried via the accompanying web portal Metabolic Atlas. Specifically, through integrative analysis of Mouse1 with RNA-sequencing data from brain tissues of transgenic mice we identified a coordinated up-regulation of lysosomal GM2 ganglioside and peptide degradation pathways which appears to be a signature metabolic alteration in Alzheimer’s disease (AD) mouse models with a phenotype of amyloid precursor protein overexpression. This metabolic shift was further validated with proteomics data from transgenic mice and cerebrospinal fluid samples from human patients. The elevated lysosomal enzymes thus hold potential to be used as a biomarker for early diagnosis of AD. Taken together, we foresee that this evolving open-source platform will serve as an important resource to facilitate the development of systems medicines and translational biomedical applications.

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Dysregulation of MS risk genes and pathways at distinct stages of disease

Neurology Neuroimmunology & Neuroinflammation ◽

10.1212/nxi.0000000000000337 ◽

2017 ◽

Vol 4 (3) ◽

pp. e337 ◽

Cited By ~ 16

Author(s):

Sundararajan Srinivasan ◽

Marco Di Dario ◽

Alessandra Russo ◽

Ramesh Menon ◽

Elena Brini ◽

...

Keyword(s):

Gene Expression ◽

Peripheral Blood ◽

Mononuclear Cells ◽

Gene List ◽

Literature Mining ◽

Specific Gene ◽

Healthy Population ◽

Gene Expressions ◽

Altered Expression ◽

Risk Genes

Objective:To perform systematic transcriptomic analysis of multiple sclerosis (MS) risk genes in peripheral blood mononuclear cells (PBMCs) of subjects with distinct MS stages and describe the pathways characterized by dysregulated gene expressions.Methods:We monitored gene expression levels in PBMCs from 3 independent cohorts for a total of 297 cases (including clinically isolated syndromes (CIS), relapsing-remitting MS, primary and secondary progressive MS) and 96 healthy controls by distinct microarray platforms and quantitative PCR. Differential expression and pathway analyses for distinct MS stages were defined and validated by literature mining.Results:Genes located in the vicinity of MS risk variants displayed altered expression in peripheral blood at distinct stages of MS compared with the healthy population. The frequency of dysregulation was significantly higher than expected in CIS and progressive forms of MS. Pathway analysis for each MS stage–specific gene list showed that dysregulated genes contributed to pathogenic processes with scientific evidence in MS.Conclusions:Systematic gene expression analysis in PBMCs highlighted selective dysregulation of MS susceptibility genes playing a role in novel and well-known pathogenic pathways.

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The Visual Opsin Gene Repertoires of Teleost Fishes: Evolution, Ecology, and Function

Annual Review of Cell and Developmental Biology ◽

10.1146/annurev-cellbio-120219-024915 ◽

2021 ◽

Vol 37 (1) ◽

Author(s):

Zuzana Musilova ◽

Walter Salzburger ◽

Fabio Cortesi

Keyword(s):

Sensory System ◽

Photoreceptor Cells ◽

Opsin Gene ◽

Annual Review ◽

Specific Gene ◽

Publication Date ◽

Teleost Fishes ◽

Opsin Genes ◽

The Rich ◽

Species Specific

Visual opsin genes expressed in the rod and cone photoreceptor cells of the retina are core components of the visual sensory system of vertebrates. Here, we provide an overview of the dynamic evolution of visual opsin genes in the most species-rich group of vertebrates, teleost fishes. The examination of the rich genomic resources now available for this group reveals that fish genomes contain more copies of visual opsin genes than are present in the genomes of amphibians, reptiles, birds, and mammals. The expansion of opsin genes in fishes is due primarily to a combination of ancestral and lineage-specific gene duplications. Following their duplication, the visual opsin genes of fishes repeatedly diversified at the same key spectral-tuning sites, generating arrays of visual pigments sensitive from the ultraviolet to the red spectrum of the light. Species-specific opsin gene repertoires correlate strongly with underwater light habitats, ecology, and color-based sexual selection. Expected final online publication date for the Annual Review of Cell and Developmental Biology, Volume 37 is October 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

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