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MicroRNAs (miRNAs) are important gene regulators, which are often deregulated in cancers. In this study, the authors analyzed the microRNAs profiles of 78 matched cancer/noncanerous liver tissues from HCC patients and 10 normal liver tissues and found that 69 miRNAs were differentially expressed between hepatocellular carcinoma (HCC) and corresponding(More)
Investigation of transcription factors (TFs) and their downstream regulated genes (targets) is a significant issue in post-genome era, which can provide a brand new vision for some vital biological process. However, information of TFs and their targets in mammalian is far from sufficient. Here, we developed an integrated TF platform (ITFP), which included(More)
MicroRNAs are a class of small endogenous noncoding RNAs which play important regulatory roles mainly by post-transcriptional depression. Finding miRNA target genes will help a lot to understand their biological functions. We developed an ensemble machine learning algorithm which helps to improve the prediction of miRNA targets. The performance was(More)
Several "head-to-head" (or "bidirectional") gene pairs have been studied in individual experiments, but genome-wide analysis of this gene organization, especially in terms of transcriptional correlation and functional association, is still insufficient. We conducted a systematic investigation of head-to-head gene organization focusing on structural(More)
Recent miRNA transfection experiments show strong evidence that miRNAs influence not only their target but also non-target genes; the precise mechanism of the extended regulatory effects of miRNAs remains to be elucidated. A hypothetical two-layer regulatory network in which transcription factors (TFs) function as important mediators of miRNA-initiated(More)
Single-stranded DNA (ssDNA) aptamers against four organophosphorus pesticides (phorate, profenofos, isocarbophos and omethoate) were simultaneously isolated from an immobilized random ssDNA library by systematic evolution of ligands by exponential enrichment (SELEX) technique. After 12 rounds of in vitro selection, five ssDNA aptamer candidates were(More)
A strand-specific transcriptome sequencing strategy, directional ligation sequencing or DeLi-seq, was employed to profile antisense transcriptome of Schizosaccharomyces pombe. Under both normal and heat shock conditions, we found that polyadenylated antisense transcripts are broadly expressed while distinct expression patterns were observed for(More)
  • Han Wu, Shuying Sun, +4 authors Jun Zhu
  • 2010
Both splicing factors and microRNAs are important regulatory molecules that play key roles in posttranscriptional gene regulation. By miRNA deep sequencing, we identified 40 miRNAs that are differentially expressed upon ectopic overexpression of the splicing factor SF2/ASF. Here we show that SF2/ASF and one of its upregulated microRNAs (miR-7) can form a(More)
SUMMARY Gene coexpression analysis was developed to explore gene interconnection at the expression level from a systems perspective, and differential coexpression analysis (DCEA), which examines the change in gene expression correlation between two conditions, was accordingly designed as a complementary technique to traditional differential expression(More)
Coordination of cell differentiation and proliferation is a key issue in the development process of multi-cellular organisms and stem cells. Here we provide evidence that the establishment of adipocyte differentiation of 3T3-L1 cells requires two processes: the licensing of an adipogenesis gene-expression program within a particular growth-arrest stage,(More)