Transcriptomes are known to organize themselves into gene co-expression clusters or modules where groups of genes display distinct patterns coordinated synchronous expression across independent biological samples. The functional significance these is suggested by the fact that highly coexpressed tend be enriched in involved common functions and processes. While widely assumed reflect close regu...

Identifying the genes that change their expressions between two conditions (such as normal versus cancer) is a crucial task that can help in understanding the causes of diseases. Differential networking has emerged as a powerful approach to detect the changes in network structures and to identify the differentially connected genes among two networks. However, existing differential network-based...

The use of high-throughput array and sequencing technologies has produced unprecedented amounts of gene expression data in central public depositories, including the Gene Expression Omnibus (GEO). The immense amount of expression data in GEO provides both vast research opportunities and data analysis challenges. Co-expression analysis of high-dimensional expression data has proven effective for...

To receive an ample amount of light, plants use elongation growth in response to vegetation shade. The combined interaction of light and hormones, including jasmonic acid (JA) signaling controls this elongation. However, the detailed molecular mechanisms underlying the response are still emerging. FAR-RED INSENSITIVE 219/JASMONATE RESISTANCE 1 (FIN219/JAR1), a cytoplasmic localized JA-conjugati...