Literature DB >> 34112883

Evaluating machine learning methodologies for identification of cancer driver genes.

Sharaf J Malebary1, Yaser Daanial Khan2.   

Abstract

Cancer is driven by distinctive sorts of changes and basic variations in genes. Recognizing cancer driver genes is basic for accurate oncological analysis. Numerous methodologies to distinguish and identify drivers presently exist, but efficient tools to combine and optimize them on huge datasets are few. Most strategies for prioritizing transformations depend basically on frequency-based criteria. Strategies are required to dependably prioritize organically dynamic driver changes over inert passengers in high-throughput sequencing cancer information sets. This study proposes a model namely PCDG-Pred which works as a utility capable of distinguishing cancer driver and passenger attributes of genes based on sequencing data. Keeping in view the significance of the cancer driver genes an efficient method is proposed to identify the cancer driver genes. Further, various validation techniques are applied at different levels to establish the effectiveness of the model and to obtain metrics like accuracy, Mathew's correlation coefficient, sensitivity, and specificity. The results of the study strongly indicate that the proposed strategy provides a fundamental functional advantage over other existing strategies for cancer driver genes identification. Subsequently, careful experiments exhibit that the accuracy metrics obtained for self-consistency, independent set, and cross-validation tests are 91.08%., 87.26%, and 92.48% respectively.

Entities:  

Year:  2021        PMID: 34112883     DOI: 10.1038/s41598-021-91656-8

Source DB:  PubMed          Journal:  Sci Rep        ISSN: 2045-2322            Impact factor:   4.379


  29 in total

Review 1.  Some remarks on predicting multi-label attributes in molecular biosystems.

Authors:  Kuo-Chen Chou
Journal:  Mol Biosyst       Date:  2013-03-28

2.  iNuc-PseKNC: a sequence-based predictor for predicting nucleosome positioning in genomes with pseudo k-tuple nucleotide composition.

Authors:  Shou-Hui Guo; En-Ze Deng; Li-Qin Xu; Hui Ding; Hao Lin; Wei Chen; Kuo-Chen Chou
Journal:  Bioinformatics       Date:  2014-02-06       Impact factor: 6.937

3.  iDHS-EL: identifying DNase I hypersensitive sites by fusing three different modes of pseudo nucleotide composition into an ensemble learning framework.

Authors:  Bin Liu; Ren Long; Kuo-Chen Chou
Journal:  Bioinformatics       Date:  2016-04-08       Impact factor: 6.937

4.  Identification of cancer driver genes based on nucleotide context.

Authors:  Felix Dietlein; Donate Weghorn; Amaro Taylor-Weiner; André Richters; Brendan Reardon; David Liu; Eric S Lander; Eliezer M Van Allen; Shamil R Sunyaev
Journal:  Nat Genet       Date:  2020-02-03       Impact factor: 38.330

5.  Unsupervised detection of cancer driver mutations with parsimony-guided learning.

Authors:  Runjun D Kumar; S Joshua Swamidass; Ron Bose
Journal:  Nat Genet       Date:  2016-09-12       Impact factor: 38.330

6.  MADGiC: a model-based approach for identifying driver genes in cancer.

Authors:  Keegan D Korthauer; Christina Kendziorski
Journal:  Bioinformatics       Date:  2015-01-07       Impact factor: 6.937

7.  iRNA-PseColl: Identifying the Occurrence Sites of Different RNA Modifications by Incorporating Collective Effects of Nucleotides into PseKNC.

Authors:  Pengmian Feng; Hui Ding; Hui Yang; Wei Chen; Hao Lin; Kuo-Chen Chou
Journal:  Mol Ther Nucleic Acids       Date:  2017-03-29

8.  iSNO-PseAAC: predict cysteine S-nitrosylation sites in proteins by incorporating position specific amino acid propensity into pseudo amino acid composition.

Authors:  Yan Xu; Jun Ding; Ling-Yun Wu; Kuo-Chen Chou
Journal:  PLoS One       Date:  2013-02-07       Impact factor: 3.240

9.  IntOGen-mutations identifies cancer drivers across tumor types.

Authors:  Abel Gonzalez-Perez; Christian Perez-Llamas; Jordi Deu-Pons; David Tamborero; Michael P Schroeder; Alba Jene-Sanz; Alberto Santos; Nuria Lopez-Bigas
Journal:  Nat Methods       Date:  2013-09-15       Impact factor: 28.547

10.  iOri-Human: identify human origin of replication by incorporating dinucleotide physicochemical properties into pseudo nucleotide composition.

Authors:  Chang-Jian Zhang; Hua Tang; Wen-Chao Li; Hao Lin; Wei Chen; Kuo-Chen Chou
Journal:  Oncotarget       Date:  2016-10-25
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  7 in total

1.  EPIMUTESTR: a nearest neighbor machine learning approach to predict cancer driver genes from the evolutionary action of coding variants.

Authors:  Saeid Parvandeh; Lawrence A Donehower; Katsonis Panagiotis; Teng-Kuei Hsu; Jennifer K Asmussen; Kwanghyuk Lee; Olivier Lichtarge
Journal:  Nucleic Acids Res       Date:  2022-07-08       Impact factor: 19.160

2.  DNAPred_Prot: Identification of DNA-Binding Proteins Using Composition- and Position-Based Features.

Authors:  Omar Barukab; Yaser Daanial Khan; Sher Afzal Khan; Kuo-Chen Chou
Journal:  Appl Bionics Biomech       Date:  2022-04-13       Impact factor: 1.664

3.  Identification of stress response proteins through fusion of machine learning models and statistical paradigms.

Authors:  Ebraheem Alzahrani; Wajdi Alghamdi; Malik Zaka Ullah; Yaser Daanial Khan
Journal:  Sci Rep       Date:  2021-11-05       Impact factor: 4.379

4.  Analyses of human cancer driver genes uncovers evolutionarily conserved RNA structural elements involved in posttranscriptional control.

Authors:  Van S Tompkins; Warren B Rouse; Collin A O'Leary; Ryan J Andrews; Walter N Moss
Journal:  PLoS One       Date:  2022-02-25       Impact factor: 3.752

5.  Machine learning techniques for identification of carcinogenic mutations, which cause breast adenocarcinoma.

Authors:  Asghar Ali Shah; Hafiz Abid Mahmood Malik; AbdulHafeez Mohammad; Yaser Daanial Khan; Abdullah Alourani
Journal:  Sci Rep       Date:  2022-07-11       Impact factor: 4.996

6.  An analytical study on the identification of N-linked glycosylation sites using machine learning model.

Authors:  Muhammad Aizaz Akmal; Muhammad Awais Hassan; Shoaib Muhammad; Khaldoon S Khurshid; Abdullah Mohamed
Journal:  PeerJ Comput Sci       Date:  2022-09-21

7.  Deep Learning Approaches for Detection of Breast Adenocarcinoma Causing Carcinogenic Mutations.

Authors:  Asghar Ali Shah; Fahad Alturise; Tamim Alkhalifah; Yaser Daanial Khan
Journal:  Int J Mol Sci       Date:  2022-09-29       Impact factor: 6.208

  7 in total

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