To facilitate the exploration of publicly available Zea mays expression data, we constructed a maize expression compendium, making use of an integration methodology and a consistent probe to gene mapping based on the 5b.60 sequence release of Z. mays. The compendium is made available through a web portal MAGIC that hosts a variety of analysis tools to easily browse and analyze the data. Our compendium is different from previous initiatives in combining expression values across different experiments by providing a consistent gene annotation across different platforms.
Download full-text PDF |
Source |
|---|---|
| http://dx.doi.org/10.1093/bioinformatics/btt739 | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
A single-cell compendium of human cerebrospinal fluid identifies disease-associated immune cell populations.
J Clin Invest
January 2025
Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA.
Single-cell transcriptomics applied to cerebrospinal fluid (CSF) for elucidating the pathophysiology of neurologic diseases has produced only a preliminary characterization of CSF immune cells. CSF derives from and borders central nervous system (CNS) tissue, allowing for comprehensive accounting of cell types along with their relative abundance and immunologic profiles relevant to CNS diseases. Using integration techniques applied to publicly available datasets in combination with our own studies, we generated a compendium with 139 subjects encompassing 135 CSF and 58 blood samples.
View Article and Find Full Text PDFGender-specific Single Transcript Level Atlas of Vasopressin and its Receptor (AVPR1a) in the Mouse Brain.
bioRxiv
December 2024
Center for Translational Medicine and Pharmacology, Icahn School of Medicine at Mount Sinai, New York, NY 10029.
Vasopressin (AVP), a nonapeptide synthesized predominantly by magnocellular hypothalamic neurons, is conveyed to the posterior pituitary the pituitary stalk, where AVP is secreted into the circulation. Known to regulate blood pressure and water homeostasis, it also modulates diverse social behaviors, such as pair-bonding, social recognition and cognition in mammals including humans. Importantly, AVP modulates social behaviors in a gender-specific manner, perhaps, due to gender differences in the distribution in the brain of AVP and its main receptor AVPR1a.
View Article and Find Full Text PDFMyristica fragrans water extract modulates multiple biological processes to pre-protect anhydrous ethanol-induced gastric ulcers via Akt/JNK/Nrf2 pathway activation.
J Ethnopharmacol
December 2024
Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100193, China; State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, China; Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100193, China; Key Laboratory of new drug discovery based on Classic Chinese medicine prescription, Chinese Academy of Medical Sciences, China; NMPA Key Laboratory for Research and Evaluation of Pharmacovigilance, China. Electronic address:
Ethnopharmacological Relevance: Myristica fragrans (Nutmeg) is a commonly used Chinese herbal medicine and edible spice. According to Pharmacopoeia of People's Republic of China, it has the effects of warming the middle and promoting qi, astringent intestines, and antidiarrheal. In the record of Compendium of Materia Medica, it is the myristica fragrans water extract (MFWE) that is utilized for therapeutic purposes of gastrointestinal disorders frequently.
View Article and Find Full Text PDFComparative transcriptomics of a generalist aphid, and a specialist aphid, reveals molecular signatures associated with diversity of their feeding behaviour and other attributes.
Front Plant Sci
December 2024
Department of Botany, University of Delhi, Delhi, India.
Introduction: Aphids are phloem sap-sucking insects and are a serious destructive pest of several crop plants. Aphids are categorized as "generalists" or "specialists" depending on their host range. (Sulz.
View Article and Find Full Text PDFA compendium of methods: Searching allele specific expression via RNA sequencing.
Gene
February 2025
Department of Bioinformatics, Central University of South Bihar, Gaya, Bihar 824236, India. Electronic address:
Diploid mammalian genome has paired alleles for each gene; typically allowing for equal expression of the two alleles within the cell/tissue. However, genetic regulatory elements and epigenetic modifications can disrupt this equality, leading to preferential expression of one allele. Examining high-confidence allele-specific expression (ASE) is vital for understanding genetic variations and their impact on major diseases like cancers and diabetes.
View Article and Find Full Text PDFWant AI Summaries of new PubMed Abstracts delivered to your In-box?
Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!