Computational Methods and Bioinformatic Tools (2002)

This chapter contains sections titled: Introduction Comparative expressed sequence tag analysis Introduction Processing expressed sequence tags prior to content analysis Gene content and annotation of expressed sequence tags Expressed sequence tags in comparative genomics In silico subtraction using clustered sets of expressed sequence tags Expressed sequence tag data repositories and cDNA clone distribution centres Data management and data mining Introduction Current situation Future development Taking part in bioinformatics Hardware and software demands Data types, structures and processing Communication structures Building a test scenario Microarray experiments Analysing the workflow – getting things done Designing the question and choosing the right tools for the answer Scaling up Strategies of data mining Data evaluation and representation Principles of query languages Data mining Custom solutions Summary Integration of heterogeneous high-throughput gene expression data Introduction Steps towards data integration Initial steps in realising data integration Conclusions Cluster analysis of gene expression profiles Introduction Information content of gene expression clusters Similarity matrices and gene expression matrices Clustering algorithms Hierarchical clustering Self-organising maps K-means Gene shaving Evaluation of gene expression clusters Conclusion Promoter finding in eukaryotic genomes Introduction Transcription regulation in eukaryotes Promoter structure Transcription factors Combinatorial nature of transcription regulation Databases on transcriptional regulation In silico study of gene transcription regulation Recognition of cis-regulatory elements Recognition of composite regulatory elements Recognition of promoters Conclusions GeneEMAC – Three-dimensional visualisation of gene expression Introduction Principles and basics of the GeneEMAC concept Specimen preparation Whole-mount in situ hybridisation Embedding Introduction of external markers Capturing of a reference image Histological sectioning Microscopy and digital image processing Image capturing Image congruencing Image segmentation Generation of a three-dimensional model Visualisations of models Examples Discussion RNA-based gene expression databases and analyses tools Introduction ASDB – The Alternative Splicing Database AsMamDB – The Alternative Splice Database of Mammals BodyMap – An anatomical gene expression database of human and mouse The CYTOMER® Gene Expression Database on human organs and cell types Database of three-dimensional visualisation of gene expression dbEST – The Database of Expressed Sequence Tags DDD – Digital Differential Display The Genexpress IMAGE Knowledge Base of the Human Genome and Transcriptomes The GencartaTM Database GEO – Gene Expression Omnibus Database GXD – The Mouse Gene Expression Database ISG Database – Interferon-Stimulated Gene Database The Kidney Development Database MAGEST – The Maboya Gene Expression Patterns and Sequence Tags Database MethDB – The DNA Methylation Database EMAGE – The Edinburgh Mouse Atlas Gene Expression Database RAD – The RNA Abundance Database The Rochester Muscle Database SAGEmap – The serial analysis of gene expression tag to gene mapping database SGD – The Saccharomyces Genome Database and its Expression Connection SMD – The Stanford Microarray Database TRIPLES – The Database of Transposon-Insertion Phenotypes, Localisation, and Expression in Saccharomyces cerevisiae UTRdb and UTRsite – The Specialised Databases of Sequences and Functional Elements of 5′ and 3′-Untranslated Regions of Eukaryotic mRNAs yMGV – The Yeast Microarray Global Viewer Protein-based gene expression databases and analyses tools Introduction to protein-based gene expression databases The Proteome Analysis Database SWISS-2DPAGE – A two-dimensional polyacrylamide gel electrophoresis database Further gene-expression databases in the internet Summary References