Links


Seminars and meetings

Seminars of the Institute for Genetics

 

Statistics / Statistical evaluation of data

McDonald, J.H. 2014. Handbook of Biological Statistics, 3rd ed. Sparky House Publishing, Baltimore, Maryland.
... and as pdf (2nd edition)

 


Maps: e.g. Mouse brain

The Allen Brain Atlas (ABA)

An interactive, genome-wide image database of gene expression in the mouse brain
(don't forget to download and install the Brain Explorer before first use....!)
citation:
E. Lein, M. Hawrylycz, et. al.: Genome-wide atlas of gene expression in the adult mouse brain..
Nature 445, pp. 168 - 176 (2007).

 


Yeast databases / AAA server

DRYGIN: Data Repository of Yeast Genetic Interactions
 
DRYGIN is a database of quantitative genetic interactions of S. cerevisiae derived from the SGA double-mutant arrays
conducted in Boone lab at Terrence Donnelly Centre for Cellular and Biochemical Research, University of Toronto.
 
Judice L.Y. Koh et al. Nucleic Acids Research, 2010, Vol. 38, Database issue D502-D507:
"DRYGIN: a database of quantitative genetic interaction networks in yeast"
Protein complexes in yeast
 
Gavin et al.: Proteome survey reveals modularity of the yeast cell machinery. Nature (2006).
SCPD - The Promoter Database of Saccharomyces cerevisiae
CYGD / Comprehensive Yeast Genome Database
Incyte: YPD Database.
Saccharomyces Genome Database
Welcome to MIPS / MIPS homepage
MEROPS - The Protease Database
Genomic Expression Programs in the Response of Yeast Cells to Environmental Changes
 
Web supplement to Gasch et al. (2000) Mol.Biol.Cell 11(12), 4241-4257
MitoP2 - Mitochondrial Proteome Database for yeast and human
Human gene database, with Integrative Annotation Validated by Full-Length cDNA Clones
Predictions of C. elegans Genetic Interactions
 
W. Zhong and P.W. Sternberg: Genome-Wide Prediction of C. elegans Genetic Interactions.
Science 311, pp. 1481 - 1484 (2006).

 


Protein analysis: sequences & structures:
Domain searches, BLAST, Prediction of Transmembrane domains etc.

HEFalMp HEFalMp: a functional map of the human genome.
Functional maps offer a way to interactively explore gene, pathway, process, and disease associations predicted from integrating hundreds of publicly available genomic datasets.
Curtis Huttenhower et al.. Exploring the human genome with functional maps, Genome Research 2009, PMID 19246570
Prediction of subcellular localisation of proteins

TargetP 1.1

TargetP 1.1 predicts the subcellular location of eukaryotic proteins. The location assignment is based on the predicted presence of any of the N-terminal presequences: chloroplast transit peptide (cTP), mitochondrial targeting peptide (mTP) or secretory pathway signal peptide (SP).

Predotar

A prediction service for identifying putative N-terminal targeting sequences

MITOPROT

Prediction of mitochondrial targeting sequences

WoLF PSORT

Protein Subcellular Localization Prediction

PsortII

Prediction of protein localization sites in cells

Mitopred

A genome-scale method for predicting mitochondrial proteins

WWW Interface to Sequence Analysis Software Tools like the Wisconsin Package

restricted access: local / Cologne

EBI European Bioinformatics Institute
NCBI National Center for Biotechnology Information
DDBJ DDBJ (DNA Data Bank of Japan)

The Protein Data Bank

Protein Data Bank Archive of macromolecular structural data

The Predict Protein Server

including direct submission to other prediction servers: Source of servers

ExPASy Proteomics Server

The ExPASy (Expert Protein Analysis System) proteomics server of the Swiss Institute of Bioinformatics (SIB) is dedicated to the analysis of protein sequences and structures as well as 2-D PAGE

Prosite Server (at ExPASy)

Direct access to the Prosite server at ExPASy

Servers dedicated to the prediction of transmembrane regions
REBASE: restriction enzymes, methylases, isoschizomers.... The Restriction Enzyme Database
The Protein Domain Database - ProDom ProDom is a comprehensive set of protein domain families automatically generated from the SWISS-PROT and TrEMBL sequence databases
The NCBI BLAST homepage The Basic Local Alignment Search Tool (BLAST) finds regions of local similarity between sequences.....

 


Literature / Papers.....

PubMed at the NCBI
ZBMed Cologne: online full-text access to many journals
Universitäts- und Stadtbücherei: online full-text access to many journals

 


Other links

Cluster of Excellence: Cellular Stress Responses in Aging-Associated Diseases (CECAD)
Zentrum für Molekulare Medizin Köln - ZMMK
Sonderforschungsbereich 635: Posttranslational control of protein function
International Graduate School in Genetics and Functional Genomics

last modification: Oct. 05, 2016