scholarly journals In-silico based identification and functional analyses of miRNAs and their targets in Cowpea (Vigna unguiculata L.)

AIMS Genetics ◽  
2017 ◽  
Vol 4 (2) ◽  
pp. 138-165 ◽  
Author(s):  
Zareen Gul ◽  
◽  
Muhammad Younas Khan Barozai ◽  
Muhammad Din
Keyword(s):  
Vigna Unguiculata ◽  
In Silico ◽  
Functional Analyses

scholarly journals Genomic Analysis of Glioblastoma Multiforme Reveals a Key Transcription Factor Signature Relevant to Prognosis and the Immune Processes

2021 ◽  
Vol 11 ◽  
Author(s):  
Zhen-Hang Li ◽  
Yan-Lei Guan ◽  
Guo-Bin Zhang
Keyword(s):  
Glioblastoma Multiforme ◽  
In Silico ◽  
Prognostic Value ◽  
Genomic Analysis ◽  
Predictive Biomarkers ◽  
Risk Scores ◽  
Functional Aspects ◽  
Number Variation ◽  
Inflammatory Processes ◽  
Functional Analyses

IntroductionGlioblastoma multiforme (GBM) develops through the accumulation of both genetic and expression alterations. Although many gene signatures have been developed as prognostic and predictive biomarkers, their robustness and functional aspects are less well characterized. The expression of most genes is regulated by transcription factors (TFs); therefore, we aimed to investigate a TF signature relevant to GBM prognosis.MethodsWe used bioinformatic methods and data from public databases to establish four clusters of key TF genes, among which cluster 1, comprising 24 TFs, showed significant prognostic value. Further in silico functional analyses were applied to investigate the utility of the TF signature.ResultsDifferent mutation and copy number variation patterns were observed between different risk score groups (based on the TF signature). In silico analyses suggested that the cases with relative high risk scores were involved in immune and inflammatory processes or pathways.ConclusionThe TF signature has significant prognostic value in different cohorts or subgroups of patients with GBM and could lead to the development immunotherapy for GBM.

scholarly journals In silico functional analyses and discovery of survivalassociated microRNA signatures in pediatric osteosarcoma

Oncoscience ◽  
2014 ◽  
Vol 1 (9) ◽  
pp. 599-608 ◽  
Author(s):  
Patricia C. Sanchez-Diaz ◽  
Tzu-Hung Hsiao ◽  
Yi Zou ◽  
Aaron J. Sugalski ◽  
Josefine Heim-Hall ◽  
...  
Keyword(s):  
In Silico ◽  
Functional Analyses ◽  
Pediatric Osteosarcoma

scholarly journals Cloning and in silico analysis of a gene encoding a putative β-carbonic anhydrase from cowpea (Vigna unguiculata L. Walp)

2013 ◽  
Vol 9 (1) ◽  
pp. 504-513 ◽  
Author(s):  
Tapan Kumar Mondal ◽  
Showkat Ahmad Ganie ◽  
Ravi Ranjan Kumar Niraj ◽  
Mukesh Kumar Rana
Keyword(s):  
Carbonic Anhydrase ◽  
Vigna Unguiculata ◽  
In Silico ◽  
In Silico Analysis ◽  
Gene Encoding ◽  
Silico Analysis

scholarly journals Whole exome sequencing identifies rare coding variants in novel human-mouse ortholog genes in African individuals diagnosed with non-syndromic hearing impairment

2020 ◽  
pp. 153537022096038
Author(s):  
Oluwafemi G Oluwole ◽  
Kevin K Esoh ◽  
Edmond Wonkam-Tingang ◽  
Noluthando Manyisa ◽  
Jean Jacques Noubiap ◽  
...  
Keyword(s):  
Exome Sequencing ◽  
Hearing Impairment ◽  
Whole Exome Sequencing ◽  
In Silico ◽  
Homozygous Variant ◽  
Whole Exome ◽  
African Populations ◽  
Mouse Orthologs ◽  
Syndromic Hearing Impairment ◽  
Functional Analyses

Physiologically, the human and murine hearing systems are very similar, justifying the extensive use of mice in experimental models for hearing impairment (HI). About 340 murine HI genes have been reported; however, whether variants in all human-mouse ortholog genes contribute to HI has been rarely investigated. In humans, nearly 120 HI genes have been identified to date, with GJB2 and GJB6 variants accounting for half of congenital HI cases, of genetic origin, in populations of European and Asian ancestries, but not in most African populations. The contribution of variants in other known genes of HI among the populations of African ancestry is poorly studied and displays the lowest pick-up rate. We used whole exome sequencing (WES) to investigate pathogenic and likely pathogenic (PLP) variants in 34 novel human-mouse orthologs HI genes, in 40 individuals from Cameroon and South Africa diagnosed with non-syndromic hearing impairment (NSHI), and compared the data to WES data of 129 ethnically matched controls. In addition, protein modeling for selected PLP gene variants, gene enrichment, and network analyses were performed. A total of 4/38 murine genes, d6wsu163e, zfp719, grp152 and minar2, had no human orthologs. WES identified three rare PLP variants in 3/34 human-mouse orthologs genes in three unrelated Cameroonian patients, namely: OCM2, c.227G>C p.(Arg76Thr) and LRGI1, c.1657G>A p.(Gly533Arg) in a heterozygous state, and a PLP variant MCPH1, c.2311C>G p.(Pro771Ala) in a homozygous state. In silico functional analyses suggest that these human-mouse ortholog genes functionally co-expressed interactions with well-established HI genes: GJB2 and GJB6. The study found one homozygous variant in MCPH1, likely to explain HI in one patient, and suggests that human-mouse ortholog variants could contribute to the understanding of the physiology of hearing in humans. Impact statement Despite, human and murine hearing system being very similar, the contribution of variants in relevant mouse-ortholog genes to hearing impairment (HI) has not been fully investigated. The contribution of variants in the known non-syndromic hearing impairment (NSHI) genes among Africans is poorly studied, suggesting that the novel gene(s) and mutations are yet to be discovered in NSHI in the African populations. Using whole exome sequencing (WES), this study identified rare candidate pathogenic and likely pathogenic (PLP) variants in 3/34 novel human-mouse ortholog genes in 3/40 individuals, with one homozygous variant, MCPH1, c.2311C>G p.(Pro771Ala), likely to explain HI in one patient. In silico functional analyses suggest that these human-mouse ortholog genes could contribute to the understanding of the physiology of hearing in humans and thus the variants identified in those genes deserve additional investigations.

In Silico Pharmaco-Gene-Informatic Identification of Insulin-Like Proteins in Plants

2013 ◽  
pp. 948-963 ◽  
Author(s):  
Koona Saradha Jyothi ◽  
G. R. Sridhar ◽  
Kudipudi Srinivas ◽  
B. Subba Rao ◽  
Allam Apparao
Keyword(s):  
Amino Acid ◽  
Human Insulin ◽  
Vigna Unguiculata ◽  
Protein Function ◽  
In Silico ◽  
Cell Envelope ◽  
Amino Acid Sequences ◽  
Jack Bean ◽  
Canavalia Ensiformis ◽  
Bauhinia Purpurea

This chapter presents an extension of the authors’ earlier work, where they showed that nucleotide/amino acid sequences related to insulin occurred in the plant kingdom. It was believed that plants did not have, nor did they need insulin, a protein hormone considered to be restricted to the animal kingdom. In the current study, the human insulin sequence was initially obtained from UniProt/SwissProt (accession no. P01308). Plant genome sequences were obtained from NCBI PubMed (Bauhinia purpurea [Gi|229412], Vigna unguiculata [P83770], and Canavalia ensiformis [Gi|7438602]. Scores were obtained from ProtFun 2.2 [http://www.cbs.dtu.dk/services/ProtFun/]. At the next stage, functions of insulin and glucokinin (insulin like proteins in plants) were predicted by the Protein Function Prediction database (http://dragon.bio.purdue.edu/pfp/index.html), followed by functional site prediction from the ELM database (http://elm.eu.org/). ProtFun predicted the following functions: human insulin (Cell envelope), Jack bean (Energy metabolism), Bauhinia purpurea(Translation). The amino acid Glycine at 32 positions was most highly conserved. Present predictions advocate the use of these sequences (QHLCGS motif) as targets for probing the other plants with lesser homology. In summary our in silico studies have suggested that Bauhinia purpurea (Purple orchid tree-BP), Vigna unguiculata (Cow pea-CP) and Canavalia ensiformis (Jack bean-JB) have conserved the important regions of the human insulin protein.

scholarly journals Identification of a novel antimicrobial peptide from amphioxus Branchiostoma japonicum by in silico and functional analyses

2015 ◽  
Vol 5 (1) ◽  
Author(s):  
Haohan Liu ◽  
Miaomiao Lei ◽  
Xiaoyuan Du ◽  
Pengfei Cui ◽  
Shicui Zhang
Keyword(s):  
Antimicrobial Peptide ◽  
In Silico ◽  
Functional Analyses

scholarly journals In silico and functional analyses of immunomodulatory peptides encrypted in the human gut metaproteome

2020 ◽  
Vol 70 ◽  
pp. 103969
Author(s):  
Noelia Cambeiro-Pérez ◽  
Claudio Hidalgo-Cantabrana ◽  
Marco Antonio Moro-García ◽  
Aitor Blanco-Míguez ◽  
Florentino Fdez-Riverola ◽  
...  
Keyword(s):  
In Silico ◽  
Human Gut ◽  
Immunomodulatory Peptides ◽  
Functional Analyses

In Silico Functional Analyses of SWEETs Reveal Cues for Their Role in AMF Symbiosis

2016 ◽  
pp. 45-58 ◽  
Author(s):  
Muhammad Sameeullah ◽  
Tijen Demiral ◽  
Noreen Aslam ◽  
Faheem Shehzad Baloch ◽  
Ekrem Gurel
Keyword(s):  
In Silico ◽  
Functional Analyses

In Silico Pharmaco-Gene-Informatic Identification of Insulin-Like Proteins in Plants

2012 ◽  
pp. 303-320
Author(s):  
Koona Saradha Jyothi ◽  
G. R. Sridhar ◽  
Kudipudi Srinivas ◽  
B. Subba Rao ◽  
Allam Apparao
Keyword(s):  
Amino Acid ◽  
Human Insulin ◽  
Vigna Unguiculata ◽  
Protein Function ◽  
In Silico ◽  
Cell Envelope ◽  
Amino Acid Sequences ◽  
Jack Bean ◽  
Canavalia Ensiformis ◽  
Bauhinia Purpurea

This chapter presents an extension of the authors’ earlier work, where they showed that nucleotide/amino acid sequences related to insulin occurred in the plant kingdom. It was believed that plants did not have, nor did they need insulin, a protein hormone considered to be restricted to the animal kingdom. In the current study, the human insulin sequence was initially obtained from UniProt/SwissProt (accession no. P01308). Plant genome sequences were obtained from NCBI PubMed (Bauhinia purpurea [Gi|229412], Vigna unguiculata [P83770], and Canavalia ensiformis [Gi|7438602]. Scores were obtained from ProtFun 2.2 [http://www.cbs.dtu.dk/services/ProtFun/]. At the next stage, functions of insulin and glucokinin (insulin like proteins in plants) were predicted by the Protein Function Prediction database (http://dragon.bio.purdue.edu/pfp/index.html), followed by functional site prediction from the ELM database (http://elm.eu.org/). ProtFun predicted the following functions: human insulin (Cell envelope), Jack bean (Energy metabolism), Bauhinia purpurea(Translation). The amino acid Glycine at 32 positions was most highly conserved. Present predictions advocate the use of these sequences (QHLCGS motif) as targets for probing the other plants with lesser homology. In summary our in silico studies have suggested that Bauhinia purpurea (Purple orchid tree-BP), Vigna unguiculata (Cow pea-CP) and Canavalia ensiformis (Jack bean-JB) have conserved the important regions of the human insulin protein.

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