Transcriptome profiling identifies genes and pathways deregulated upon Floxuridine treatment in colorectal cancer cells harboring GOF mutant p53
Publication date: Available online 17 March 2016 Source:Genomics Data Author(s): Arindam Datta, Sanjib Dey, Pijush Das, Sk. Kayum Alam, Susanta Roychoudhury Mutation in TP53 is a common genetic alteration in human cancers. Certain tumor associated p53 missense mutants acquire gain-of-function (GOF) properties and confer oncogenic phenotypes including enhanced chemoresistance. The colorectal cancers (CRC) harboring mutant p53 are generally aggressive in nature and difficult to treat. To identify a potential gene expression signature of GOF mutant p53-driven acquired chemoresistance in CRC, we performed transcr...
Source: Genomics Data - March 18, 2016 Category: Genetics & Stem Cells Source Type: research
Analyzing the temporal regulation of translation efficiency in mouse liver
Publication date: Available online 18 March 2016 Source:Genomics Data Author(s): Peggy Janich, Alaaddin Bulak Arpat, Violeta Castelo-Szekely, David Gatfield Mammalian physiology and behavior follow daily rhythms that are orchestrated by endogenous timekeepers known as circadian clocks. Rhythms in transcription are considered the main mechanism to engender rhythmic gene expression, but important roles for posttranscriptional mechanisms have recently emerged as well (reviewed in Lim and Allada (2013) [1]). We have recently reported on the use of ribosome profiling (RPF-seq), a method based on the high-throughput ...
Source: Genomics Data - March 18, 2016 Category: Genetics & Stem Cells Source Type: research
RNA sequencing analysis of gene expression regulated by the transcription factor SlZFP2 during early fruit development
Publication date: Available online 10 March 2016 Source:Genomics Data Author(s): Lin Weng, Fangfang Zhao, Rong Li, Han Xiao [Briefly describe the contents of the Data in Brief article. Tell the reader the repository and reference number for the data in the abstract to.] The transcription factor SlZFP2 (Solanum lycopersicum Zinc Finger Protein 2) regulates ABA biosynthesis during fruit development. To reveal the regulatory network of this transcription factor, we conducted a high-throughput RNA-seq to identify differentially expressed genes in 2 dpa (days post anthesis) fruits from a representative RNAi line in ...
Source: Genomics Data - March 10, 2016 Category: Genetics & Stem Cells Source Type: research
Complete genome sequence of a giant Vibrio phage ValKK3 infecting Vibrio alginolyticus
Publication date: Available online 10 March 2016 Source:Genomics Data Author(s): Tamrin M. Lal, Motohiko Sano, Kishio Hatai, Julian Ransangan This paper describes the complete sequence of a giant lytic marine myophage, Vibrio phage ValKK3 that is specific to Vibrio alginolyticus ATCC® 17749™. Vibrio phage ValKK3 was subjected to whole genome sequencing on MiSeq sequencing platform and annotated using Blast2Go. The complete sequence of ValKK3 genome was deposited in DBBJ/EMBL/GenBank under accession number KP671755. (Source: Genomics Data)
Source: Genomics Data - March 10, 2016 Category: Genetics & Stem Cells Source Type: research
Draft genome sequence of Psychrobacter sp. ENNN9_III, a strain isolated from water in a polluted temperate estuarine system (Ria de Aveiro, Portugal)
Publication date: June 2016 Source:Genomics Data, Volume 8 Author(s): Jaqueline Conceição Meireles Gomes, Juliana Simão Nina de Azevedo, Adonney Allan de Oliveira Veras, Jorianne Thyeska Castro Alves, Isabel Henriques, António Correia, Artur Luiz da Costa da Silva, Adriana Ribeiro Carneiro The genus Psychrobacter includes Gram-negative coccobacilli that are non-pigmented, oxidase-positive, non-motile, psychrophilic or psychrotolerant, and halotolerant. Psychrobacter strain ENNN9_III was isolated from water in a polluted temperate estuarine system, contaminated with hydrocarbons and heavy metals. The...
Source: Genomics Data - March 3, 2016 Category: Genetics & Stem Cells Source Type: research
A fuzzy based feature selection from independent component subspace for machine learning classification of microarray data
Publication date: June 2016 Source:Genomics Data, Volume 8 Author(s): Rabia Aziz, C.K. Verma, Namita Srivastava Feature (gene) selection and classification of microarray data are the two most interesting machine learning challenges. In the present work two existing feature selection/extraction algorithms, namely independent component analysis (ICA) and fuzzy backward feature elimination (FBFE) are used which is a new combination of selection/extraction. The main objective of this paper is to select the independent components of the DNA microarray data using FBFE to improve the performance of support vector machin...
Source: Genomics Data - March 3, 2016 Category: Genetics & Stem Cells Source Type: research
Role(s) of IL-2 inducible T cell kinase and Bruton's tyrosine kinase in mast cell response to lipopolysaccharide
Publication date: June 2016 Source:Genomics Data, Volume 8 Author(s): Weishan Huang, Avery August Mast cells play critical roles during immune responses to the bacterial endotoxin lipopolysaccharide (LPS) that can lead to fatal septic hypothermia [1–3]. IL-2 inducible T cell kinase (ITK) and Bruton's tyrosine kinase (BTK) are non-receptor tyrosine kinases that act downstream of numerous receptors, and have been shown to modulate mast cell responses downstream of FcεRIα [4], however, their roles in regulating mast cell responses to endotoxic stimuli were unclear. We found that the absence of ITK and BTK alters t...
Source: Genomics Data - February 29, 2016 Category: Genetics & Stem Cells Source Type: research
Genomic analysis of xCT-regulatory network in KSHV+ primary effusion lymphomas
Publication date: June 2016 Source:Genomics Data, Volume 8 Author(s): Zhiqiang Qin, Yueyu Cao, Lu Dai Kaposi's sarcoma-associated herpesvirus (KSHV) is the etiological agent of primary effusion lymphoma (PEL), a rapidly progressing malignancy mostly arising in HIV-infected patients Chen et al. (2007) [1]. Even under conventional chemotherapy, PEL continues to portend nearly 100% mortality within several months, which urgently requires novel therapeutic strategies. We have previously demonstrated that targeting xCT, an amino acid transporter for cystine/glutamate exchange, induces significant PEL cell apoptosis th...
Source: Genomics Data - February 29, 2016 Category: Genetics & Stem Cells Source Type: research
Transcriptional profiling of macrophage and tumor cell interactions in vitro
Publication date: June 2016 Source:Genomics Data, Volume 8 Author(s): Filip Roudnicky, Maija Hollmén Macrophages are important mediators of tumor progression and their function is broadly influenced by different microenvironmental stimuli. To understand the molecular basis of the tumor-supporting role of macrophages in aggressive breast cancer we co-cultured human peripheral monocytes with two breast cancer cell lines representing distinct aggressive cellular phenotype and transcriptionally profiled the changes occurring in both cells during in vitro activated crosstalk. Here we provide a detailed description of t...
Source: Genomics Data - February 29, 2016 Category: Genetics & Stem Cells Source Type: research
Next generation sequencing (NGS) database for tandem repeats with multiple pattern 2°-shaft multicore string matching
Publication date: March 2016 Source:Genomics Data, Volume 7 Author(s): Chinta Someswara Rao, S. Viswanadha Raju Next generation sequencing (NGS) technologies have been rapidly applied in biomedical and biological research in recent years. To provide the comprehensive NGS resource for the research, in this paper , we have considered 10 loci/codi/repeats TAGA, TCAT, GAAT, AGAT, AGAA, GATA, TATC, CTTT, TCTG and TCTA. Then we developed the NGS Tandem Repeat Database (TandemRepeatDB) for all the chromosomes of Homo sapiens, Callithrix jacchus, Chlorocebus sabaeus, Gorilla gorilla, Macaca fascicularis, Macaca mulatta, No...
Source: Genomics Data - February 23, 2016 Category: Genetics & Stem Cells Source Type: research
Computational gene expression profiling under salt stress reveals patterns of co-expression
Publication date: March 2016 Source:Genomics Data, Volume 7 Author(s): Sanchita, Ashok Sharma Plants respond differently to environmental conditions. Among various abiotic stresses, salt stress is a condition where excess salt in soil causes inhibition of plant growth. To understand the response of plants to the stress conditions, identification of the responsible genes is required. Clustering is a data mining technique used to group the genes with similar expression. The genes of a cluster show similar expression and function. We applied clustering algorithms on gene expression data of Solanum tuberosum showing d...
Source: Genomics Data - February 2, 2016 Category: Genetics & Stem Cells Source Type: research
Mutation-based structural modification and dynamics study of amyloid beta peptide (1–42): An in-silico-based analysis to cognize the mechanism of aggregation
Publication date: March 2016 Source:Genomics Data, Volume 7 Author(s): Pritam Kumar Panda, Abhaysinha Satish Patil, Priyam Patel, Hetalkumar Panchal Alzheimer's disease is the prevalent cause of premature senility, a progressive mental disorder due to degeneration in brain and deposition of amyloid β peptide (1–42, a misfolded protein) in the form of aggregation that prevails for a prolonged time and obstructs every aspect of life. One of the primary hallmarks of the neuropathological disease is the accretion of amyloid β peptide in the brain that leads to Alzheimer's disease, but the mechanism is still a m...
Source: Genomics Data - January 20, 2016 Category: Genetics & Stem Cells Source Type: research
IL-22 regulation of functional gene expression in salivary gland cells
Publication date: March 2016 Source:Genomics Data, Volume 7 Author(s): Tegan N. Lavoie, Wendy C. Carcamo, Arun Wanchoo, Ashok Sharma, Afife Gulec, Kathleen M. Berg, Carol M. Stewart, Cuong Q. Nguyen TH17 cells and their associated signature cytokines, IL-17 and IL-22, are highly elevated in primary Sjögren's syndrome (pSjS). The levels of IL-22 present in sera showed significant correlations with many disease parameters, specifically hyposalivation, anti-SSB, anti-SSA/SSB, hypergammaglobulinemia and rheumatoid factor. The present study aims to examine the biological function of IL-22 on human salivary ...
Source: Genomics Data - January 13, 2016 Category: Genetics & Stem Cells Source Type: research
High-quality ChIP-seq analysis of MBD3 in human breast cancer cells
Publication date: March 2016 Source:Genomics Data, Volume 7 Author(s): Takashi Shimbo, Motoki Takaku, Paul A. Wade Chromatin accessibility is tightly regulated by multiple factors/mechanisms to establish different cell type-specific gene expression programs from a single genome. Dysregulation of this process can lead to diseases including cancer. The Mi-2/nucleosome remodeling and deacetylase (NuRD) complex is thought to orchestrate chromatin structure using its intrinsic nucleosome remodeling and histone deacetylase activities. However, the detailed mechanisms by which the NuRD complex regulates chromatin struct...
Source: Genomics Data - January 12, 2016 Category: Genetics & Stem Cells Source Type: research
Genome-wide identification and analysis of mRNA expression in fibroblasts, ES cells, and iPS cells
Publication date: March 2016 Source:Genomics Data, Volume 7 Author(s): Hiroyuki Hirai, Nobuaki Kikyo Genome-wide expression patterns of mRNA were compared between mouse embryonic fibroblasts (MEFs), embryonic stem cells (ESCs), and various types of induced pluripotent stem cells (iPSCs). iPSCs were established and maintained using modified Oct4 with or without exogenous leukemia inhibitory factor (LIF) and used to identify mRNAs that were potentially involved in the LIF-independence. The data have been deposited in the NCBI's Gene Expression Omnibus (GEO) database with the accession number GSE65563. (Source: Genomics Data)
Source: Genomics Data - January 12, 2016 Category: Genetics & Stem Cells Source Type: research
