FiRe is a user-friendly Excel macro designed to survey microarray data rapidly. This software interactively assembles data from different experiments and produces lists of candidate genes according to patterns of gene expression. Furthermore, macros bundled with FiRe can compare lists of genes, merge information from different spreadsheets, link candidates to information available from web-based databases, and produce heat-maps for easy visualization of microarray data. FiRe is freely available at http://www.unifr.ch/plantbio/FiRe/main.html .
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http://dx.doi.org/10.1016/j.tplants.2006.05.009 | DOI Listing |
Womens Health (Lond)
January 2025
Department of Pathology, Faculdade de Medicina, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil.
Background: Breast cancer (BC) is a significant burden on healthcare systems, especially in low- and middle-income countries where access to diagnosis and treatment is challenging.
Objectives: The purpose of this study was to assess the diagnostic accuracy and cost using tissue microarray (TMA) instead of traditional immunohistochemical (IHC) evaluation for estrogen receptor (ER), progesterone receptor (PR), human epidermal growth factor 2 (HER2), and the proliferation marker Ki-67 and BC subtyping within the Brazilian public health system.
Design: This is a retrospective cohort study comparing TMA slides with traditional whole-slide evaluation for IHC markers in 242 BC cases.
Cancer research has been significantly advanced by the integration of transcriptomic data through high-throughput sequencing technologies like RNA sequencing (RNA-seq). This paper reviews the transformative impact of transcriptomics on understanding cancer biology, focusing on the use of extensive datasets such as The Cancer Genome Atlas (TCGA) and Genotype-Tissue Expression (GTEx). While transcriptomic data provides crucial insights into gene expression patterns and disease mechanisms, the analysis is fraught with technical and biological biases.
View Article and Find Full Text PDFInt J Med Sci
January 2025
Department of Otolaryngology, Head and Neck Surgery, Kaohsiung Veterans General Hospital, Kaohsiung 813, Taiwan.
Sinonasal inverted papilloma (SNIP) is characterized by a high recurrence rate and potential for malignant transformation. Although metabolic reprogramming plays a role in benign neoplasms, the specific metabolic pathways and biomarkers involved in SNIP pathogenesis remain unclear. RNA sequencing on paired SNIP and normal tissues identified altered genes with enzyme annotations and metabolic pathways by intersecting our cohort data (GSE270193, N=2) with the GSE193016 (N=4) dataset using Ingenuity Pathway Analysis.
View Article and Find Full Text PDFFront Pharmacol
December 2024
State Key Laboratory of Oncology in South China, Department of Gastric Surgery, Sun Yat-Sen University Cancer Center, Guangdong Provincial Clinical Research Center for Cancer, Guangzhou, China.
Aim: Programmed cell death (PCD) critically influences the tumor microenvironment (TME) and is intricately linked to tumor progression and patient prognosis. This study aimed to develop a novel prognostic indicator and marker of drug sensitivity in patients with gastric cancer (GC) based on PCD.
Methods: We analyzed genes associated with 14 distinct PCD patterns using bulk transcriptome data and clinical information from TCGA-STAD for model construction with univariate Cox regression and LASSO regression analyses.
Nature
January 2025
Department of Neurosurgery, Yale School of Medicine, New Haven, CT, USA.
Cerebral cortex development in humans is a highly complex and orchestrated process that is under tight genetic regulation. Rare mutations that alter gene expression or function can disrupt the structure of the cerebral cortex, resulting in a range of neurological conditions. Lissencephaly ('smooth brain') spectrum disorders comprise a group of rare, genetically heterogeneous congenital brain malformations commonly associated with epilepsy and intellectual disability.
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