On the sensitivity of feature ranked lists for large-scale biological data by Danuta Gaweł, Krzysztof Fujarewicz

Subjects: Get full text

Comprehensive analysis of differential mRNA and circRNA profiles in primary and metastatic pancreatic neuroendocrine tumors by Gang Li, Jing Zhang, Bentuo Zhang, Dan Wang, Zequn Wang, Yan Pan, Lijie Ma

Subjects: Get full text

Generalizability of machine learning models for diabetes detection a study with nordic islet transplant and PIMA datasets by Dinesh Chellappan, Harikumar Rajaguru

Subjects: Get full text

Insights into the signal transduction pathways of mouse lung type II cells revealed by transcription factor profiling in the transcriptome by Chilakamarti V. Ramana

Subjects: Get full text

RatDEGdb: a knowledge base of differentially expressed genes in the rat as a model object in biomedical research by I. V. Chadaeva, S. V. Filonov, K. A. Zolotareva, B. M. Khandaev, N. I. Ershov, N. L. Podkolodnyy, R. V. Kozhemyakina, D. A. Rasskazov, A. G. Bogomolov, E. Yu. Kondratyuk, N. V. Klimova, S. G. Shikhevich, M. A.  Ryazanova, L. A. Fedoseeva, О. Е. Redina, О. S. Kozhevnikova, N. A. Stefanova, N. G. Kolosova, A. L. Markel, M. P. Ponomarenko, Yu. D. Oshchepkov

Subjects: Get full text

Gene Coexpression Network Comparison via Persistent Homology by Ali Nabi Duman, Harun Pirim

“…Persistent homology, a topological data analysis (TDA) method, is applied to microarray data sets. Although there are a few papers referring to TDA methods in microarray analysis, the usage of persistent homology in the comparison of several weighted gene coexpression networks (WGCN) was not employed before to the very best of our knowledge. …”
Get full text

Gene Expression Changes in Venous Segment of Overflow Arteriovenous Fistula by Yasuhiro Hashimoto, Akiko Okamoto, Hisao Saitoh, Shingo Hatakeyama, Takahiro Yoneyama, Takuya Koie, Chikara Ohyama

“…Total RNA was extracted from the venous tissue samples, and gene expression between the 2 groups was compared using Whole Human Genome DNA microarray 44 K. Microarray data were analyzed by GeneSpring GX software and Ingenuity Pathway Analysis. …”
Get full text

circRNA Expression Profile in Dental Pulp Stem Cells during Odontogenic Differentiation by Ming Chen, Yeqing Yang, Junkai Zeng, Zilong Deng, Buling Wu

“…Total RNA was extracted after 14 days of culture, and then, microarray analysis was performed to measure the differential expressions of circRNAs. …”
Get full text

A Diagnosis of Maternal 22q Duplication and Mosaic Deletion following Prenatal Cell-Free DNA Screening by Melissa A. Hicks, Emilie Lalonde, Jessica Zoladz, Bernard Gonik, Salah Ebrahim

“…The patient reported a similar cfDNA result in a previous pregnancy; however postnatal chromosomal microarray on that child identified an atypical 22q11.21 microduplication. …”
Get full text

An Interstitial 4q Deletion with a Mosaic Complementary Ring Chromosome in a Child with Dysmorphism, Linear Skin Pigmentation, and Hepatomegaly by J. Carter, H. Brittain, D. Morrogh, N. Lench, J. J. Waters

“…Confirmation of the origin of the ring chromosome was obtained by FISH analysis which identified that the ring chromosome contained material from the deleted region of chromosome 4 and was therefore complementary to the 21.6 Mb deletion. Further microarray studies in the proband using a different microarray platform showed no evidence of mosaicism. …”
Get full text

A Robust Hybrid Approach Based on Estimation of Distribution Algorithm and Support Vector Machine for Hunting Candidate Disease Genes by Li Li, Hongmei Chen, Chang Liu, Fang Wang, Fangfang Zhang, Lihua Bai, Yihan Chen, Luying Peng

“…Microarray data are high dimension with high noise ratio and relatively small sample size, which makes it a challenge to use microarray data to identify candidate disease genes. …”
Get full text

Evolutionary Approach for Relative Gene Expression Algorithms by Marcin Czajkowski, Marek Kretowski

“…A Relative Expression Analysis (RXA) uses ordering relationships in a small collection of genes and is successfully applied to classiffication using microarray data. As checking all possible subsets of genes is computationally infeasible, the RXA algorithms require feature selection and multiple restrictive assumptions. …”
Get full text

Identification of Biomarkers for Esophageal Squamous Cell Carcinoma Using Feature Selection and Decision Tree Methods by Chun-Wei Tung, Ming-Tsang Wu, Yu-Kuei Chen, Chun-Chieh Wu, Wei-Chung Chen, Hsien-Pin Li, Shah-Hwa Chou, Deng-Chyang Wu, I-Chen Wu

“…Previous studies utilized microarray techniques to identify more than one hundred genes; however, it is desirable to identify a small set of biomarkers for clinical use. …”
Get full text

On-Chip DNA Assembly via Dielectrophoresis by Xichuan Rui, Lin-Sheng Wu, Xin Zhao

“…While there exist several microarray-based oligo synthesis technologies, on-chip gene assembly has yet to be demonstrated. …”
Get full text

Robust Semiparametric Optimal Testing Procedure for Multiple Normal Means by Peng Liu, Chong Wang

“…In high-dimensional gene expression experiments such as microarray and RNA-seq experiments, the number of measured variables is huge while the number of replicates is small. …”
Get full text

The Influence of Cell Source and Donor Age on the Tenogenic Potential and Chemokine Secretion of Human Mesenchymal Stromal Cells by Weronika Zarychta-Wiśniewska, Anna Burdzińska, Katarzyna Zielniok, Marta Koblowska, Kamila Gala, Piotr Pędzisz, Roksana Iwanicka- Nowicka, Anna Fogtman, Aleksandra Aksamit, Agnieszka Kulesza, Aleksandra Zołocińska, Leszek Pączek

“…Based on microarray results, 8 factors were chosen for further evaluation. …”
Get full text

Survival Analysis by Penalized Regression and Matrix Factorization by Yeuntyng Lai, Morihiro Hayashida, Tatsuya Akutsu

“…Because every disease has its unique survival pattern, it is necessary to find a suitable model to simulate followups. DNA microarray is a useful technique to detect thousands of gene expressions at one time and is usually employed to classify different types of cancer. …”
Get full text

A Case of 17q21.31 Microduplication and 7q31.33 Microdeletion, Associated with Developmental Delay, Microcephaly, and Mild Dysmorphic Features by Adrian Mc Cormack, Juliet Taylor, Leah Te Weehi, Donald R. Love, Alice M. George

“…Concurrent cryptic microdeletion and microduplication syndromes have recently started to reveal themselves with the advent of microarray technology. Analysis has shown that low-copy repeats (LCRs) have allowed chromosome regions throughout the genome to become hotspots for nonallelic homologous recombination to take place. …”
Get full text

Pseudohypoparathyroidism type 1A presenting as short stature and congenital hypothyroidism by Ragini Kondetimmanahalli, Jane Lynch, Gary Francis, Heather Gardner, Radhika Pillai

“…Screening laboratory studies for endocrine disorders, a skeletal survey if skeletal disproportion is evident, a karyotype or microarray (microarray favored if developmental delay is also present) and genetic testing for monogenic disorders will lead to a specific diagnosis in an additional subset of short children. …”
Get full text

Phenotypic alterations in articulating joint cells: Role of mechanically loaded MSC secretome by Yann D. Ladner, Ursula Menzel, Keith Thompson, Angela R. Armiento, Martin J. Stoddart

“…Previously, we employed a small-panel microarray to demonstrate differences within conditioned medium (CM) of MSCs that were mechanically stimulated within a joint-mimicking bioreactor and their unloaded controls.This study analyzed the proteomic content within CM from 4 week mechanically loaded MSCs with a larger protein microarray. …”
Get full text