PepC: proteomics software for identifying differentially expressed proteins based on spectral counting
نویسندگان
چکیده
منابع مشابه
RegStatGel: proteomic software for identifying differentially expressed proteins based on 2D gel images
UNLABELLED Image analysis of two-dimensional gel electrophoresis is a key step in proteomic workflow for identifying proteins that change under different experimental conditions. Since there are usually large amount of proteins and variations shown in the gel images, the use of software for analysis of 2D gel images is inevitable. We developed open-source software with graphical user interface ...
متن کاملBioinformatics analysis of differentially expressed proteins in prostate cancer based on proteomics data
We mined the literature for proteomics data to examine the occurrence and metastasis of prostate cancer (PCa) through a bioinformatics analysis. We divided the differentially expressed proteins (DEPs) into two groups: the group consisting of PCa and benign tissues (P&b) and the group presenting both high and low PCa metastatic tendencies (H&L). In the P&b group, we found 320 DEPs, 20 of which w...
متن کاملMultivariate methods for identifying differentially expressed genes
Motivation: Univariate testing procedures remain the most common way to identify differentially expressed genes (DEGs). Univariate techniques suffer from the multiple comparison problem and reduced power, because they fail to account for gene interaction. Motivated by these issues, we adopt a multivariate procedure. Namely, we utilize the sup-norm test, which was specifically developed for high...
متن کاملIdentifying differentially expressed subnetworks with MMG
BACKGROUND Mixture model on graphs (MMG) is a probabilistic model that integrates network topology with (gene, protein) expression data to predict the regulation state of genes and proteins. It is remarkably robust to missing data, a feature particularly important for its use in quantitative proteomics. A new implementation in C and interfaced with R makes MMG extremely fast and easy to use and...
متن کاملIdentifying differentially expressed genes with siggenes
In this vignette, we show how the functions contained in the R package siggenes can be used to perform both the Significance Analysis of Microarrays (SAM) proposed by Tusher et al. (2001) and the Empirical Bayes Analysis of Microarrays (EBAM) suggested by Efron et al. (2001).
متن کاملذخیره در منابع من
با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید
ژورنال
عنوان ژورنال: Bioinformatics
سال: 2010
ISSN: 1367-4803,1460-2059
DOI: 10.1093/bioinformatics/btq171