Comparative analysis of tissue-specific genes in maize based on machine learning models: CNN performs technically best, LightGBM performs biologically soundest
Z Wang, Y Zhu, Z Liu, H Li, X Tang, Y Jiang - Frontiers in Genetics, 2023 - frontiersin.org
Introduction: With the advancement of RNA-seq technology and machine learning, training
large-scale RNA-seq data from databases with machine learning models can generally …
large-scale RNA-seq data from databases with machine learning models can generally …
Genome-wide discovery of tissue-specific genes in Maize
F Lin, H Bao, J Yang, Y Liu, H Dai, H Zhao - Plant Molecular Biology …, 2016 - Springer
Abstract Analysis of spatial and temporal gene expression pattern is instrumental to
elucidation of gene networks and molecular mechanisms of tissue development. It also …
elucidation of gene networks and molecular mechanisms of tissue development. It also …
MCENet: a database for maize conditional co-expression network and network characterization collaborated with multi-dimensional omics levels
T Tian, Q You, H Yan, W Xu, Z Su - Journal of Genetics and Genomics, 2018 - Elsevier
Maize (Zea mays) is the most widely grown grain crop in the world, playing important roles in
agriculture and industry. However, the functions of maize genes remain largely unknown …
agriculture and industry. However, the functions of maize genes remain largely unknown …
Maize gene atlas developed by RNA sequencing and comparative evaluation of transcriptomes based on RNA sequencing and microarrays
Transcriptome analysis is a valuable tool for identification and characterization of genes and
pathways underlying plant growth and development. We previously published a microarray …
pathways underlying plant growth and development. We previously published a microarray …
AgriSeqDB: an online RNA-Seq database for functional studies of agriculturally relevant plant species
Background The genome-wide expression profile of genes in different tissues/cell types and
developmental stages is a vital component of many functional genomic studies …
developmental stages is a vital component of many functional genomic studies …
Genome-wide identification of housekeeping genes in maize
In the wake of recent progress of high throughput transcriptome profiling technologies,
extensive housekeeping gene mining has been conducted in humans. However, very few …
extensive housekeeping gene mining has been conducted in humans. However, very few …
Distinct tissue-specific transcriptional regulation revealed by gene regulatory networks in maize
J Huang, J Zheng, H Yuan, K McGinnis - BMC plant biology, 2018 - Springer
Abstract Background Transcription factors (TFs) are proteins that can bind to DNA
sequences and regulate gene expression. Many TFs are master regulators in cells that …
sequences and regulate gene expression. Many TFs are master regulators in cells that …
Predicting tissue-specific mRNA and protein abundance in maize: a machine learning approach
Machine learning and modeling approaches have been used to classify protein sequences
for a broad set of tasks including predicting protein function, structure, expression, and …
for a broad set of tasks including predicting protein function, structure, expression, and …
Plant Gene Expression Network
M Asari, A Kitazumi, E Nambara… - … Omics: Advances in …, 2022 - cabidigitallibrary.org
The expression profile of a given gene represents the changes in expression levels and it
can be established from a variety of experiments including different tissues, organs …
can be established from a variety of experiments including different tissues, organs …
RNA-seq analyses of multiple meristems of soybean: novel and alternative transcripts, evolutionary and functional implications
Background Soybean is one of the most important crops, providing large amounts of dietary
proteins and edible oil, and is also an excellent model for studying evolution of duplicated …
proteins and edible oil, and is also an excellent model for studying evolution of duplicated …