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 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 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.

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

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

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

scholarly journals Circular RNA detection identifies circPSEN1 alterations in brain specific to Autosomal Dominant Alzheimer Disease

2021 ◽  
Author(s):  
Hsiang-Han Chen ◽  
Abdallah Eteleeb ◽  
Ciyang Wang ◽  
Maria Victoria Fernandez ◽  
John P. Budde ◽  
...  
Keyword(s):  
Gene Expression ◽  
Signaling Pathway ◽  
In Silico ◽  
Autosomal Dominant ◽  
Age At Onset ◽  
Wnt Signaling Pathway ◽  
Circular Rna ◽  
Circular Rnas ◽  
Mutation Carriers ◽  
Functional Analyses

Background: Autosomal-dominant Alzheimer's disease (ADAD) is caused by pathogenic mutations in APP, PSEN1, and PSEN2, which usually lead to an early age at onset (<65). Circular RNAs are a family of non-coding RNAs highly expressed in the nervous system and especially in synapses. We aimed to investigate differences in brain gene expression of linear and circular transcripts from the three ADAD genes in controls, sporadic AD, and ADAD. Methods: We obtained and sequenced RNA from brain cortex using standard protocols. Linear counts were obtained using the TOPMed pipeline; circular counts, using python package DCC. After stringent quality control (QC), we obtained the counts for PSEN1, PSEN2 and APP genes. Only circPSEN1 passed QC. We used DESeq2 to compare the counts across groups, correcting for biological and technical variables. Finally, we performed in-silico functional analyses using the Circular RNA interactome website and DIANA mirPath software. Results: Our results show significant differences in gene counts of circPSEN1 in ADAD individuals, when compared to sporadic AD and controls (ADAD=22, AD=274, Controls=25 - ADADvsCO: log2FC=0.786, p=9.08x10-05, ADADvsAD: log2FC=0.576, p=2.00x10-03). The high gene counts are contributed by two circPSEN1 species (hsa_circ_0008521 and hsa_circ_0003848). No significant differences were observed in linear PSEN1 gene expression between cases and controls, indicating that this finding is specific to the circular forms. In addition, the high circPSEN1 levels do not seem to be specific to PSEN1 mutation carriers; the counts are also elevated in APP and PSEN2 mutation carriers. In-silico functional analyses suggest that circPSEN1 is involved in several pathways such as axon guidance (p=3.39x10-07), hippo signaling pathway (p=7.38x10-07), lysine degradation (p=2.48x10-05) or Wnt signaling pathway (p=5.58x10-04) among other KEGG pathways. Additionally, circPSEN1 counts were able to discriminate ADAD from sporadic AD and controls with an AUC above 0.70. Conclusions: Our findings show the differential expression of circPSEN1 is increased in ADAD. Given the biological function previously ascribed to circular RNAs and the results of our in-silico analyses, we hypothesize that this finding might be related to neuroinflammatory events that lead or that are caused by the accumulation of amyloid-beta.

scholarly journals Structural-functional analyses of textile dye degrading azoreductase, laccase and peroxidase: A comparative in silico study

2020 ◽  
Vol 43 ◽  
pp. 48-54 ◽  
Author(s):  
Shrabana Sarkar ◽  
Aparna Banerjee ◽  
Nibedita Chakraborty ◽  
Karuna Soren ◽  
Priyanka Chakraborty ◽  
...  
Keyword(s):  
In Silico ◽  
Textile Dye ◽  
In Silico Study ◽  
Functional Analyses
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