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Junmin Liu

Publications and source records attributed to Junmin Liu.

5 recordsLinked to original sources
PubMed2006

A simple spreadsheet-based, MIAME-supportive format for microarray data: MAGE-TAB.

BACKGROUND: Sharing of microarray data within the research community has been greatly facilitated by the development of the disclosure and communication standards MIAME and MAGE-ML by the MGED Society. However, the complexity of the MAGE-ML format has made its use impractical for laboratories lacking dedicated bioinformatics support. RESULTS: We propose a simple tab-delimited, spreadsheet-based format, MAGE-TAB, which will become a part of the MAGE microarray data standard and can be used for annotating and communicating microarray data in a MIAME compliant fashion. CONCLUSION: MAGE-TAB will enable laboratories without bioinformatics experience or support to manage, exchange and submit well-annotated microarray data in a standard format using a spreadsheet. The MAGE-TAB format is self-contained, and does not require an understanding of MAGE-ML or XML.

Computational Biology↗
PubMed2006

EPConDB: a web resource for gene expression related to pancreatic development, beta-cell function and diabetes.

EPConDB (http://www.cbil.upenn.edu/EPConDB) is a public web site that supports research in diabetes, pancreatic development and beta-cell function by providing information about genes expressed in cells of the pancreas. EPConDB displays expression profiles for individual genes and information about transcripts, promoter elements and transcription factor binding sites. Gene expression results are obtained from studies examining tissue expression, pancreatic development and growth, differentiation of insulin-producing cells, islet or beta-cell injury, and genetic models of impaired beta-cell function. The expression datasets are derived using different microarray platforms, including the BCBC PancChips and Affymetrix gene expression arrays. Other datasets include semi-quantitative RT-PCR and MPSS expression studies. For selected microarray studies, lists of differentially expressed genes, derived from PaGE analysis, are displayed on the site. EPConDB provides database queries and tools to examine the relationship between a gene, its transcriptional regulation, protein function and expression in pancreatic tissues.

Animals↗
PubMed2005

A practical false discovery rate approach to identifying patterns of differential expression in microarray data.

SUMMARY: Searching for differentially expressed genes is one of the most common applications for microarrays, yet statistically there are difficult hurdles to achieving adequate rigor and practicality. False discovery rate (FDR) approaches have become relatively standard; however, how to define and control the FDR has been hotly debated. Permutation estimation approaches such as SAM and PaGE can be effective; however, they leave much room for improvement. We pursue the permutation estimation method and describe a convenient definition for the FDR that can be estimated in a straightforward manner. We then discuss issues regarding the choice of statistic and data transformation. It is impossible to optimize the power of any statistic for thousands of genes simultaneously, and we look at the practical consequences of this. For example, the log transform can both help and hurt at the same time, depending on the gene. We examine issues surrounding the SAM 'fudge factor' parameter, and how to handle these issues by optimizing with respect to power.

Algorithms↗
PubMed2003

Expression of beta-human chorionic gonadotropin genes in renal cell cancer and benign renal disease tissues.

To study the expression of beta-human chorionic gonadotropin (beta hCG) genes in renal cell carcinomas (RCC) and benign renal disease tissues, nested reverse transcription-polymerase chain reaction (RT-PCR) and restriction endonuclease analysis were employed to detect the expression of beta hCG genes in 44 cases of RCC tissues and 24 cases of benign renal disease tissues. It was found that 52% RCC samples revealed positive for beta hCG mRNA expression. Positive rate in advanced stage and poorly differentiated RCC was higher, but there was no significant difference. The positive rate of beta hCG mRNA expression was 54% in 24 cases of benign renal tissues, including 3 cases out of 6 polycystic kidneys, 7 cases out of 13 renal atrophies, 2 cases out of 2 oncocytomas and 1 case out of 2 pyonephrotic kidneys. beta 7 was most frequently transcribed subtype gene independent on the histology. These findings suggested beta hCG gene transcription is not only involved in RCC but also in benign renal diseases.

Adult↗