Co‐expression tools for plant biology: opportunities for hypothesis generation and caveats

B Usadel, T Obayashi, M Mutwil… - Plant, cell & …, 2009 - Wiley Online Library
Gene co‐expression analysis has emerged in the past 5 years as a powerful tool for gene
function prediction. In essence, co‐expression analysis asks the question 'what are the …

Dynamics of global transcriptome in bovine matured oocytes and preimplantation embryos

M Misirlioglu, GP Page, H Sagirkaya… - Proceedings of the …, 2006 - National Acad Sciences
Global activation of the embryonic genome is the most critical event in early mammalian
development. After fertilization, a rich supply of maternal proteins and RNAs support …

Transcriptional coordination of the metabolic network in Arabidopsis

H Wei, S Persson, T Mehta… - Plant …, 2006 - academic.oup.com
Patterns of coexpression can reveal networks of functionally related genes and provide
deeper understanding of processes requiring multiple gene products. We performed an …

Transcriptome analysis of bull spermatozoa: implications for male fertility

JM Feugang, N Rodriguez-Osorio, A Kaya… - Reproductive …, 2010 - Elsevier
Spermatozoa deliver more than the paternal genome into the oocyte; they also carry
remnant messenger RNA from spermatogenesis. The RNA profiles of spermatozoa from …

Microarray analysis

GP Page, SO Zakharkin, K Kim, T Mehta, L Chen… - Topics in …, 2007 - Springer
Microarrays and related technologies have allowed investigators to ask biological questions
in far greater detail than has previously been possible. Microarrays had a troubled …

Wnt pathway genes in osteoporosis and osteoarthritis: differential expression and genetic association study

J Velasco, MT Zarrabeitia, JR Prieto… - Osteoporosis …, 2010 - Springer
In comparison with hip fractures, increased expression of genes in the Wnt pathway and
increased Wnt activity were found in bone samples and osteoblast cultures from patients …

CressExpress: a tool for large-scale mining of expression data from Arabidopsis

V Srinivasasainagendra, GP Page, T Mehta… - Plant …, 2008 - academic.oup.com
CressExpress is a user-friendly, online, coexpression analysis tool for Arabidopsis
(Arabidopsis thaliana) microarray expression data that computes patterns of correlated …

[HTML][HTML] Identification of molecular distinctions between normal breast-associated fibroblasts and breast cancer-associated fibroblasts

A Sadlonova, DB Bowe, Z Novak, S Mukherjee… - Cancer …, 2009 - Springer
Stromal fibroblasts influence the behavior of breast epithelial cells. Fibroblasts derived from
normal breast (NAF) inhibit epithelial growth, whereas fibroblasts from breast carcinomas …

Exploring tomato gene functions based on coexpression modules using graph clustering and differential coexpression approaches

A Fukushima, T Nishizawa, M Hayakumo… - Plant …, 2012 - academic.oup.com
Gene-to-gene coexpression analysis provides fundamental information and is a promising
approach for predicting unknown gene functions in plants. We investigated various …

The effect of insulin on expression of genes and biochemical pathways in human skeletal muscle

X Wu, J Wang, X Cui, L Maianu, B Rhees, J Rosinski… - Endocrine, 2007 - Springer
To study the insulin effects on gene expression in skeletal muscle, muscle biopsies were
obtained from 20 insulin sensitive individuals before and after euglycemic hyperinsulinemic …