Census of orthologous genes and self-organizing maps of biologically relevant transcriptional patterns in chickens (Gallus gallus)

Wu, Xiaolin; Griffin, Kirsten B.; Garcia, Matthew; Michal, Jennifer J.; Xiao, Qi; Wright, Raymond W.; Jiang, Zhihua

doi:10.1016/j.gene.2004.06.038

Cited by 11 publications

(13 citation statements)

References 24 publications

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“…We are the first to report DE genes that are common between PRRSV infection and 22 human infectious diseases. In particular, PRRSV infection of PAMs induced DE of 65,33,30,28,23,23, and 21 genes that are commonly associated with influenza infection, tuberculosis, HTLV-I infection, Herpes simplex infection HIV Infection, leishmaniasis, and toxoplasmosis, respectively.…”

Section: Discussionmentioning

confidence: 99%

Reactomes of Porcine Alveolar Macrophages Infected with Porcine Reproductive and Respiratory Syndrome Virus

et al. 2013

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Porcine reproductive and respiratory syndrome (PRRS) has devastated pig industries worldwide for many years. It is caused by a small RNA virus (PRRSV), which targets almost exclusively pig monocytes or macrophages. In the present study, five SAGE (serial analysis of gene expression) libraries derived from 0 hour mock-infected and 6, 12, 16 and 24 hours PRRSV-infected porcine alveolar macrophages (PAMs) produced a total 643,255 sequenced tags with 91,807 unique tags. Differentially expressed (DE) tags were then detected using the Bayesian framework followed by gene/mRNA assignment, arbitrary selection and manual annotation, which determined 699 DE genes for reactome analysis. The DAVID, KEGG and REACTOME databases assigned 573 of the DE genes into six biological systems, 60 functional categories and 504 pathways. The six systems are: cellular processes, genetic information processing, environmental information processing, metabolism, organismal systems and human diseases as defined by KEGG with modification. Self-organizing map (SOM) analysis further grouped these 699 DE genes into ten clusters, reflecting their expression trends along these five time points. Based on the number one functional category in each system, cell growth and death, transcription processes, signal transductions, energy metabolism, immune system and infectious diseases formed the major reactomes of PAMs responding to PRRSV infection. Our investigation also focused on dominant pathways that had at least 20 DE genes identified, multi-pathway genes that were involved in 10 or more pathways and exclusively-expressed genes that were included in one system. Overall, our present study reported a large set of DE genes, compiled a comprehensive coverage of pathways, and revealed system-based reactomes of PAMs infected with PRRSV. We believe that our reactome data provides new insight into molecular mechanisms involved in host genetic complexity of antiviral activities against PRRSV and lays a strong foundation for vaccine development to control PRRS incidence in pigs.

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Section: Discussionmentioning

confidence: 99%

Reactomes of Porcine Alveolar Macrophages Infected with Porcine Reproductive and Respiratory Syndrome Virus

et al. 2013

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“…ESTs have served as the “unigene” resources at the National Center for Biotechnology Information (NCBI) to infer approximate expression patterns by tissue, age, and health status for more than 140 species (http://www.ncbi.nlm.nih.gov/unigene). ESTs have also been used to examine exclusively expressed genes, co-expressed genes, house-keeping genes and genes that are differentially expressed due to different conditions or diseases [17–21]. …”

Section: Whole Transcriptome Shotgun Sequencingmentioning

confidence: 99%

Whole transcriptome analysis with sequencing: methods, challenges and potential solutions

Jiang

Zhou

et al. 2015

Cell. Mol. Life Sci.

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Whole transcriptome analysis plays an essential role in deciphering genome structure and function, identifying genetic networks underlying cellular, physiological, biochemical and biological systems and establishing molecular biomarkers that respond to diseases, pathogens and environmental challenges. Here, we review transcriptome analysis methods and technologies that have been used to conduct whole transcriptome shotgun sequencing or whole transcriptome tag/target sequencing analyses. We focus on how adaptors/linkers are added to both 5′ and 3′ ends of mRNA molecules for cloning or PCR amplification before sequencing. Challenges and potential solutions are also discussed. In brief, next generation sequencing platforms have accelerated releases of the large amounts of gene expression data. It is now time for the genome research community to assemble whole transcriptomes of all species and collect signature targets for each gene/transcript, and thus use known genes/transcripts to determine known transcriptomes directly in the near future.

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“…Inc.) was then used to depict the biological relation of the 12 single bovine tissues/organs in view of their transcriptomes. A statistic for estimating the transcriptional LOD (logarithm of the odds, base 10) score (Wu et al 2004) was used to choose genes that are preferentially expressed in the tissue of interest: LOD > 3, which means that, for a gene to be qualified as preferentially expressed, the likelihood that it was expressed higher in the tissue of interest than in the control should be >10 3 times greater than if it was expressed equally in both tissues.…”

Section: Statistical Analysesmentioning

confidence: 99%

“…In the present study, we used the transcriptional LOD score (Wu et al 2004) to compare expression level of a gene between 2 different sources. This statistic differed from the R statistic (Stekel et al 2000), as the transcriptional LOD score distinguishes the nature of expression level whereas the R statistic would give a similar value of a logarithm likelihood ratio to genes with similar deviations from the control, whether positive or negative.…”

Section: Transcriptional Lod Scorementioning

confidence: 99%

Comparative gene-based in silico analysis of transcriptomes in different bovine tissues and (or) organs

Jiang

Xiao

Garcia

et al. 2004

Genome

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A gene-based approach was used to annotate 322,168 cattle expressed sequence tags (ESTs) based on human genes in order to census the transcriptomes, analyze their expression similarities, and identify genes preferentially expressed in different bovine tissues and (or) organs. Of the 34,157 human coding genes used in a standalone BLAST search, 14,928 could be matched with provisional orthologous sequences in a total of 230,135 bovine ESTs. The remaining 92,033 bovine ESTs were estimated to represent an additional 5970 genes in cattle. On average, approximately 8600 genes were estimated to be expressed in a single tissue and (or) organ and 13,000 in a pooled tissue library. On the basis of the estimated numbers of genes, no more than 3% of genes would be missed when approximately 34,000 ESTs were sequenced from a single tissue and (or) organ library and approximately 40,000 ESTs from a pooled source, respectively. Cluster analyses of the gene expression patterns among 12 single tissues and (or) organs in cattle revealed that their expression similarities would depend on physiological functions. In addition, a total of 1502 genes were identified as preferentially expressed genes in these 12 single tissues and (or) organs with LOD (logarithm of the odds, base 10) > or = 3.0. Therefore, our study provides some insights for further investigating the developmental and functional relations of various tissues and organs in mammals.

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Census of orthologous genes and self-organizing maps of biologically relevant transcriptional patterns in chickens (Gallus gallus)

Cited by 11 publications

References 24 publications

Reactomes of Porcine Alveolar Macrophages Infected with Porcine Reproductive and Respiratory Syndrome Virus

Reactomes of Porcine Alveolar Macrophages Infected with Porcine Reproductive and Respiratory Syndrome Virus

Whole transcriptome analysis with sequencing: methods, challenges and potential solutions

Comparative gene-based in silico analysis of transcriptomes in different bovine tissues and (or) organs

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