Map of GeneExpress system 

Gateway to GeneExpress system

1. Transcription Regulation (TRRD)

   1. Database of genes: TRRDGENES4
   2. Database of transcription factor binding sites: TRRDSITES4
   3. Database of transcription factors: TRRDFAC4
   4. Database of expression patterns: TRRDEXP4
   5. Database of references: TRRDBIB4
   6. TRRD Viewer

2. Site Activity Prediction (ACTIVITY)

   1. Database on activities of DNA/RNA functional sites
   2. Database on context-dependent physical-chemical and conformational properties of DNA
   3. Database on weight functions for activity prediction
   4. Database on references
   5. Knowledge base on functional site activities
   6. Program package for prediction of activity of functional sites on the basis of their nucleotide sequences

3. Site Recognition

   1. B-DNA Video

      1. PROPERTY, database on DNA/RNA functional sites activities
      2. SAMPLES, database on sets of transcription factor binding sites and other regulatory regions
      3. FEATURES, database on the sequence-dependent conformational features of  transcription factor binding sites
      4. PROFILES, database on significant physico-chemical properties of transcription factor binding sites
      5. Program package for calculating profiles of conformational and physical-chemical features of B-DNA

   2. Consensus and weight matrices (ConsFreg)

      1. Database on sets of transcription factor binding sites
      2. Database on aligned sets of transcription factor binding sites
      3. Knowledge base on consensuses of transcription factor binding sites
      4. Knowledge base on weight matrix of transcription factor binding sites
      5. Program package for recognition of transcription factor binding sites by consensuses
      6. Program package for recognition of transcription factor binding sites by frequency matrices

   3. Transcription factor binding site recognition (TFBSR)

      1. Program for constructing recognition groups
      2. Program for recognizing transcription factor binding sites using recognition groups
      3. Database on sets of transcription factor binding sites
   4. SELEX_DB
      1. SELEX_DB: a database on selected randomized DNA/RNA sequences
      2. SELEX_BIB: a database on annotated in SELEX_DB papers
      3. SELEX_TOOLS: a database on computer programs for recognition of sites accumulated in SELEX_DB

4. GeneNetworks (GeneNet)

   1. Database on cells and cell lines
   2. Database on genes
   3. Database on proteins and their complexes
   4. Database on substances
   5. Database on processes
   6. Database on relations between the gene network components
   7. Database on schemes of the gene networks
   8. Database on references
   9. GeneNet Viewer

5. mRNA Translation (Leader mRNA)

   1. Leader_SQ, database on 5'UTR of mRNAs with the level of their translational efficiency
   2. Leader_KN, knowledge base on characteristics of 5'UTR of mRNAs essential for translation efficiency
   3. Database on references
   4. Program package for predicting the level of mRNA translation on the basis of their nucleotide sequences

6. Regulatory Proteins (CRASP)

   1. Analysis of pairwise positional correlations in multiple alignments
   2. Analysis of protein integral physico-chemichal properties

7. Nucleosomal Organization of DNA

   1. PROPERTY, database on context-dependent physical-chemical and conformational properties of DNA
   2. Samples of nucleosome binding sites
   3. Recon  program to recognize nucleosome binding sites
   4. DNA property viewer
   5. FEATURES, knowledge base on significant conformational and physical-chemical features of nucleosome binding sites
   6. PROFILES, knowledge base on profiles of physical-chemical features of nucleosome binding sites

8. Other Programs as a Part of GeneExpress System

   1. RNA secondary structure prediction by genetic algorithm
   2. Searching for oligonucleotide repeats in DNA sequences
   3. Generator of C codes of consensuses and frequency matrices from aligned sequences of DNA/RNA sites
   4. Program for nucleosome binding site recognition

(resources listed by alphabet are available)

© 1997-99, IC&G   SB RAS, Laboratory of Theoretical Genetics