Zhenjun Hu,Joseph Mellor,Charles DeLisi
Zhenjun Hu
The VisANT tool, accessible from any recent Java-enabled browser, is a platform-independent, flexible, Web-enabled program for quick and simple construction, visualization, and analysis of molecular and higher order networks based on functi...
Lincoln D Stein
Lincoln D Stein
There is considerable interest in the bioinformatics community in creating pathway databases. The Reactome project (a collaboration between Cold Spring Harbor Laboratory and the European Bioinformatics Institute) is one such pathway databas...
Identifying functional sites based on prediction of charged group behavior [0.03%]
基于电荷团簇行为预测的功能位点识别方法
Mary Jo Ondrechen
Mary Jo Ondrechen
This protocol describes the implementation and interpretation of THEMATICS, a simple computational predictor of functional information for proteins from the three-dimensional structure. This method is based on the computation of the electri...
Deepak Kaushal,Clayton W Naeve
Deepak Kaushal
This unit assumes the reader is familiar with the Spotfire environment, has successfully installed Spotfire, and has uploaded and prepared data for analysis. It presents numerous methods for analyzing microarray data. Specifically, the firs...
Deepak Kaushal,Clayton W Naeve
Deepak Kaushal
This unit strictly focuses on data preparation within Spotfire. Microarray data exist in a variety of formats, which often depend on the particular array technology and detection instruments used. The first protocols in this unit describe l...
Deepak Kaushal,Clayton W Naeve
Deepak Kaushal
Spotfire DecisionSite for Functional Genomics (referred to here as Spotfire) is a powerful data mining and visualization application with use in many disciplines. This unit provides an overview of Spotfire's utility in analyzing gene expres...
Integrating whole-genome expression results into metabolic networks with Pathway Processor [0.03%]
采用Pathway Processor方法将基因组范围的表达结果整合入代谢网络中
Duccio Cavalieri,Paul Grosu
Duccio Cavalieri
Genes never act alone in a biological system, but participate in a cascade of networks. As a result, analyzing microarray data from a pathway perspective leads to a new level of understanding the system. The authors' group has recently deve...
Using GenMAPP and MAPPFinder to view microarray data on biological pathways and identify global trends in the data [0.03%]
使用GenMAPP和MAPPFinder查看生物通路的DNA微阵列数据并识别这些数据中的普遍趋势
Kam D Dahlquist
Kam D Dahlquist
GenMAPP (Gene MicroArray Pathway Profiler) is a free, stand-alone computer program designed for viewing and analyzing gene expression data on MAPPs representing biological pathways or any other functional grouping of genes. A MAPP is a spec...
Microarray data visualization and analysis with the Longhorn Array Database (LAD) [0.03%]
使用长角阵列数据库(LAD)对微数组数据进行可视化和分析
Patrick J Killion,Vishwanath R Iyer
Patrick J Killion
The wide availability and use of DNA microarrays has brought the power of whole-genome functional characterization to a large variety of research environments. Microarrays, however, also introduce significant infrastructural and analytical ...
Using PEBBLE for the evolutionary analysis of serially sampled molecular sequences [0.03%]
用PEBBLE对连续采样的分子序列进行进化分析
Matthew Goode,Allen G Rodrigo
Matthew Goode
The PEBBLE (Phylogenetics, Evolutionary Biology, and Bioinformatics in a moduLar Environment) application is a relative newcomer to the field of phylogenetic applications. Although designed as a customizable generalist application, PEBBLE w...