DEG: a database of essential genes

“…BLASTP (http://blast.ncbi.nlm.nih.gov/Blast.cgi) analysis was carried out for the nonredundant proteome against the proteome of human genome tax id: 9606. Proteins with an E-value (expectation value) of 10 -4 were eliminated, assuming that they have a certain level of homology with the host genome (Zhang et al, 2004). The homologous proteins were eliminated and nonhomologous proteins were separated for further analysis.…”

Section: Methodsmentioning

confidence: 99%

“…Further the non-homologous proteins were analysed using DEG (http://tubic.tju.edu.cn/deg/), which includes all the essential genes currently available (Zhang et al, 2004). A random E-value was kept at 10G 4 and the minimum bit-score cut-off value of 100, BLOSUM62 matrix and gapped alignment mode were selected to identify the essential genes (Rathi et al, 2009).…”

Section: Methodsmentioning

confidence: 99%

Identification of Putative Therapeutic Targets in Candida tropicalis: An in silico Approach

Ravinaraya¹,

Coico²,

Sundar³

2015

Trends in Bioinformatics

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The prolonged use of antibiotics results in drug resistance in pathogenic microorganisms. This necessitates the identification of novel drug targets that are useful for the development of effective antimicrobial drugs. In the post-genomic era, computational tools and methods have contributed immensely in identifying such novel targets, thereby accelerating the drug discovery process. In the present study, an extensive in silico analysis of the proteome of the pathogenic yeast, Candida tropicalis was performed to identify potential drug targets. The complete proteome of C. tropicalis retrieved from Uniprot was analysed using the CD-HIT algorithm followed by BLAST for eliminating proteins homologous to human proteome. The selected proteins were then analyzed using DEG database for identifying critical genes for the survival. The identified essential proteins were subjected to pathway analysis using KEGG to predict their involvement in metabolism. This approach resulted in the identification of 20 potential drug targets present in C. tropicalis.

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“…In the first comparison, a subtractive genomics approach was applied to pathogen proteins from unique pathways. The BLAST search (Altschul et al, 1990) based on essentiality criteria was performed against the Database of Essential Genes (DEG version 10.9) (Zhang et al, 2004), which hosts records of essential genomic elements critical for an organism's survival, such as protein-coding genes and non-coding RNAs, among bacteria, archaea, and eukaryotes. An expectation value (e-value) threshold of 0.005 was used as filtering criteria for BLAST hits; with C. jejuni and Helicobacter pylori as background organisms against which a similarity search for identification of essential genes was performed.…”

Section: Subtractive Genomics and Identification Of Essential Non-hommentioning

confidence: 99%

Novel Drug Targets for Food-Borne PathogenCampylobacter jejuni: An Integrated Subtractive Genomics and Comparative Metabolic Pathway Study

Mehla

Ramana

2015

OMICS: A Journal of Integrative Biology

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Campylobacters are a major global health burden and a cause of food-borne diarrheal illness and economic loss worldwide. In developing countries, Campylobacter infections are frequent in children under age two and may be associated with mortality. In developed countries, they are a common cause of bacterial diarrhea in early adulthood. In the United States, antibiotic resistance against Campylobacter is notably increased from 13% in 1997 to nearly 25% in 2011. Novel drug targets are urgently needed but remain a daunting task to accomplish. We suggest that omics-guided drug discovery is timely and worth considering in this context. The present study employed an integrated subtractive genomics and comparative metabolic pathway analysis approach. We identified 16 unique pathways from Campylobacter when compared against H. sapiens with 326 non-redundant proteins; 115 of these were found to be essential in the Database of Essential Genes. Sixty-six proteins among these were non-homologous to the human proteome. Six membrane proteins, of which four are transporters, have been proposed as potential vaccine candidates. Screening of 66 essential non-homologous proteins against DrugBank resulted in identification of 34 proteins with drug-ability potential, many of which play critical roles in bacterial growth and survival. Out of these, eight proteins had approved drug targets available in DrugBank, the majority serving crucial roles in cell wall synthesis and energy metabolism and therefore having the potential to be utilized as drug targets. We conclude by underscoring that screening against these proteins with inhibitors may aid in future discovery of novel therapeutics against campylobacteriosis in ways that will be pathogen specific, and thus have minimal toxic effect on host. Omics-guided drug discovery and bioinformatics analyses offer the broad potential for veritable advances in global health relevant novel therapeutics.

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DEG: a database of essential genes

Cited by 467 publications

References 11 publications

In Silico Structural and Functional Prediction of Phaseolus vulgaris Hypothetical Protein PHA VU_004G136400g

In Silico Structural and Functional Prediction of Phaseolus vulgaris Hypothetical Protein PHA VU_004G136400g

Identification of Putative Therapeutic Targets in Candida tropicalis: An in silico Approach

Novel Drug Targets for Food-Borne PathogenCampylobacter jejuni: An Integrated Subtractive Genomics and Comparative Metabolic Pathway Study

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