Global prediction of tissue-specific gene expression and context-dependent gene networks in Caenorhabditis elegans.
Tissue-specific gene expression plays a fundamental role in metazoan biology and is an important aspect of many complex diseases. Nevertheless, an organism-wide map of tissue-specific expression remains elusive due to difficulty in obtaining these data experimentally. Here, we leveraged existing whole-animal Caenorhabditis elegans microarray data representing diverse conditions and developmental stages to generate accurate predictions of tissue-specific gene expression and experimentally validated these predictions. These patterns of tissue-specific expression are more accurate than existing high-throughput experimental studies for nearly all tissues; they also complement existing experiments by addressing tissue-specific expression present at particular developmental stages and in small tissues. We used these predictions to address several experimentally challenging questions, including the identification of tissue-specific transcriptional motifs and the discovery of potential miRNA regulation specific to particular tissues. We also investigate the role of tissue context in gene function through tissue-specific functional interaction networks. To our knowledge, this is the first study producing high-accuracy predictions of tissue-specific expression and interactions for a metazoan organism based on whole-animal data.
Chikina
Maria D
MD
Department of Molecular Biology, Princeton University, Princeton, New Jersey, USA.
Huttenhower
Curtis
C
Murphy
Coleen T
CT
Troyanskaya
Olga G
OG
D000465:Algorithms; D000818:Animals; D001185:Artificial Intelligence; D001483:Base Sequence; D017173:Caenorhabditis elegans / Q000235:genetics* / Q000378:metabolism; D003198:Computer Simulation; D003627:Data Interpretation, Statistical; D050980:GATA Transcription Factors / Q000235:genetics / Q000378:metabolism; D020869:Gene Expression Profiling; D005786:Gene Expression Regulation; D053263:Gene Regulatory Networks; D049452:Green Fluorescent Proteins / Q000235:genetics / Q000378:metabolism; D035683:MicroRNAs / Q000235:genetics / Q000378:metabolism; D008957:Models, Genetic; D020411:Oligonucleotide Array Sequence Analysis; D011401:Promoter Regions, Genetic; D015203:Reproducibility of Results; D012689:Sequence Homology, Nucleic Acid
D050980:GATA Transcription Factors; D035683:MicroRNAs; D049452:Green Fluorescent Proteins