AIMC Topic: Gene Expression Profiling

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XGSA: A statistical method for cross-species gene set analysis.

Bioinformatics (Oxford, England) Sep 1, 2016
MOTIVATION: Gene set analysis is a powerful tool for determining whether an experimentally derived set of genes is statistically significantly enriched for genes in other pre-defined gene sets, such as known pathways, gene ontology terms, or other ex...
Datasets as Topic Species Specificity Gene Ontology Vertebrates Conserved Sequence Software Animals Gene Expression Profiling Regeneration
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Biomarker discovery based on BBHA and AdaboostM1 on microarray data for cancer classification.

Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference Aug 1, 2016
In this paper, a new approach based on Binary Black Hole Algorithm (BBHA) and Adaptive Boosting version Ml (AdaboostM1) is proposed for finding genes that can classify the group of cancers correctly. In this approach, BBHA is used to perform gene sel...
Gene Expression Profiling Computational Biology Humans Decision Trees Algorithms Statistics as Topic Biomarkers, Tumor Oligonucleotide Array Sequence Analysis Neoplasms
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FMLNCSIM: fuzzy measure-based lncRNA functional similarity calculation model.

Oncotarget Jul 19, 2016
Accumulating experimental studies have indicated the influence of lncRNAs on various critical biological processes as well as disease development and progression. Calculating lncRNA functional similarity is of high value in inferring lncRNA functions...
Gene Expression Profiling Transcriptome Gene Regulatory Networks Computational Biology Fuzzy Logic Humans Computer Simulation RNA, Long Noncoding
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Support Vector Machine Based on microRNA Expression Profiles to Predict Histological Origin of Ampullary Carcinoma: Case Report of a Patient Affected From Adenocarcinoma of the Papilla of Vater With Lynch Syndrome.

Pancreas Apr 1, 2016
Adenocarcinomas of Vater's papilla (PVAC) may originate from either the pancreatic duct or the intestinal epithelium. Conflicting data have been reported about the frequency of the 2 anatomical entities and their influence on patients' prognosis. To ...
Humans Gene Expression Regulation, Neoplastic Adenocarcinoma Ampulla of Vater Support Vector Machine MicroRNAs Pancreatic Ducts Prognosis Male Female Pancreatic Neoplasms Middle Aged Young Adult Gene Expression Profiling Carcinoma Adult Adolescent Family Health Child Pedigree Colorectal Neoplasms, Hereditary Nonpolyposis
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Evaluation of Machine Learning Algorithm Utilization for Lung Cancer Classification Based on Gene Expression Levels.

Asian Pacific journal of cancer prevention : APJCP Jan 1, 2016
BACKGROUND: Lung cancer remains one of the most common cancers in the world, both in terms of new cases (about 13% of total per year) and deaths (nearly one cancer death in five), because of the high case fatality. Errors in lung cancer type or malig...
Algorithms Small Cell Lung Carcinoma Databases, Factual Carcinoma, Squamous Cell Biomarkers, Tumor Gene Expression Profiling Humans Case-Control Studies Machine Learning Lung Neoplasms Adenocarcinoma Support Vector Machine Decision Trees
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KNOWLEDGE-ASSISTED APPROACH TO IDENTIFY PATHWAYS WITH DIFFERENTIAL DEPENDENCIES.

Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing Jan 1, 2016
We have previously developed a statistical method to identify gene sets enriched with condition-specific genetic dependencies. The method constructs gene dependency networks from bootstrapped samples in one condition and computes the divergence betwe...
Models, Statistical Glioblastoma Knowledge Bases Likelihood Functions Gene Expression Profiling Humans Systems Integration Gene Regulatory Networks Algorithms Computational Biology Brain Neoplasms Signal Transduction Databases, Genetic
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Intraoperative Diagnosis Support Tool for Serous Ovarian Tumors Based on Microarray Data Using Multicategory Machine Learning.

International journal of gynecological cancer : official journal of the International Gynecological Cancer Society Jan 1, 2016
OBJECTIVES: Serous borderline ovarian tumors (SBOTs) are a subtype of serous ovarian carcinoma with atypical proliferation. Frozen-section diagnosis has been used as an intraoperative diagnosis tool in supporting the fertility-sparing surgery by diag...
Real-Time Polymerase Chain Reaction Reverse Transcriptase Polymerase Chain Reaction RNA, Messenger Gene Expression Regulation, Neoplastic Support Vector Machine Survival Rate Biomarkers, Tumor Gene Expression Profiling Monitoring, Intraoperative Carcinoma, Ovarian Epithelial Immunoenzyme Techniques Neoplasms, Glandular and Epithelial Cystadenocarcinoma, Serous Databases, Genetic Ovarian Neoplasms Predictive Value of Tests Blotting, Western Neoplasm Staging Humans Machine Learning Prognosis Female
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LncRNA ontology: inferring lncRNA functions based on chromatin states and expression patterns.

Oncotarget Nov 24, 2015
Accumulating evidences suggest that long non-coding RNAs (lncRNAs) perform important functions. Genome-wide chromatin-states area rich source of information about cellular state, yielding insights beyond what is typically obtained by transcriptome pr...
Cell Line, Tumor Gene Regulatory Networks Gene Ontology RNA, Messenger Humans Chromatin Hep G2 Cells Models, Genetic Algorithms Promoter Regions, Genetic Transcription Initiation Site Cell Line Cells, Cultured Lysine RNA, Long Noncoding Neoplasms HeLa Cells K562 Cells Gene Expression Profiling Methylation Histones
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Distinct Transcriptional and Anti-Mycobacterial Profiles of Peripheral Blood Monocytes Dependent on the Ratio of Monocytes: Lymphocytes.

EBioMedicine Nov 1, 2015
The ratio of monocytes and lymphocytes (ML ratio) in peripheral blood is associated with tuberculosis and malaria disease risk and cancer and cardiovascular disease outcomes. We studied anti-mycobacterial function and the transcriptome of monocytes i...
Disease Susceptibility Binding Sites Leukocyte Count Interferons Humans Mycobacterium Male Disease Resistance Signal Transduction Female Gene Expression Profiling Transcription Factors Young Adult Transcriptome Adult Tuberculosis Protein Binding Lymphocytes Monocytes
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Feature selection using feature dissimilarity measure and density-based clustering: application to biological data.

Journal of biosciences Oct 1, 2015
Reduction of dimensionality has emerged as a routine process in modelling complex biological systems. A large number of feature selection techniques have been reported in the literature to improve model performance in terms of accuracy and speed. In ...
Multigene Family Datasets as Topic Oligonucleotide Array Sequence Analysis Multifactor Dimensionality Reduction Computational Biology Humans Algorithms Cluster Analysis Neoplasms Parkinson Disease Gene Expression Profiling Gene Expression Arrhythmias, Cardiac
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