Allegro: Analyzing expression and sequence in concert to discover regulatory programs. Halperin Y et al. A major goal of system biology is the characterization of transcription factors and microRNAs (miRNAs) and the transcriptional programs they regulate. We present Allegro, a method for de-novo discovery of cis-regulatory transcriptional programs through joint analysis of genome-wide expression data and promoter or 3' UTR sequences. The algorithm uses a novel log-likelihood-based, non-parametric model to describe the expression pattern shared by a group of co-regulated genes. We show that Allegro is more accurate and sensitive than existing techniques, and can simultaneously analyze multiple expression datasets with more than 100 conditions. We apply Allegro on datasets from several species and report on the transcriptional modules it uncovers. Our analysis reveals a novel motif over-represented in the promoters of genes highly expressed in murine oocytes. The present gene id highly expressed in the oocyte and has a unique promoter motif.
General function
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Cellular localization
Cytoplasmic
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Ovarian function
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Expression regulated by
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Ovarian localization
Oocyte
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Bovine mater-like NALP9 is an oocyte marker gene.
Dalbies-Tran R, et al .
Physiologie de la Reproduction et des Comportements, UMR 6175 Institut National de la Recherche Agronomique/Centre National de la Recherche Scientifique/Universite Francois Rabelais de Tours/Haras Nationaux, Nouzilly, France.
We have cloned and sequenced the bovine NALP9 cDNA, which contains a 2991 bp long open reading frame with 76% homology to its human counterpart. The putative 996 amino acids protein presents the domain organization typical of the Nacht, Leucine rich repeat and Pyrin domain containing (NALP) family that includes the maternal effect factor MATER. By reverse transcription coupled to polymerase chain reaction, we have analyzed expression of NALP9 in a panel of somatic and gonadic tissues and during in vitro preimplantation development. The transcript was detected exclusively in testis and ovary, and at a remarkably high level in the oocyte from antral follicles. NALP9 mRNA remained present after in vitro maturation and fertilization, and was detected in embryos, but transcription was not reactivated at the maternal to embryo transition. Thus NALP9 is characterized as a novel oocyte marker gene in cattle.