文档介绍：Integration of Heterogeneous Informations Sources for Proteomics and Transcriptomics
Steffen Möller
University of Rostock
Proteome Center
Data Flow and Motivation
List of genes products with changed expression level
Description of variants of genes
Sample
Sample
Group A
Sample
Sample
Group Z
...
Sample Selection
Preparation
Analysis
Measurements
Question
Interpretation
Data available online
Grouping of samples in homogeneous groups
Portioning and preparation of samples
Data derived from a preparation
DNA/RNA sequencing
Affymetrix Microarrays
2DE Gels
(Tandem) mass spectrometry
External bioinformatics databases
Internal extensions to the munication of ideas between researchers
Lab-internal information
Measurements
Aids for Interpretation of Data
Organisation of Samples
Access of MS Spectra
MASCOT peptide identification
MS/MS fragment sequencing
Addition to external data sources
Genes discussed among researchers
Figure 1: The figure shows the integration of protein expression as derived from the analysis of the gel with the RNA expression from a chip experiment, represented as a linearly scaled yellow bar. The spot volume is equivalently depicted as in red, the area in green and the peak intensity in blue.
Overview on Identified Spots on Gel
Integration of Protein expression levels
Spot Volume
Spot Area
Spot Peak intensity
with RNA expression levels
from Affymetrix chips
Application of Agent Technology
Automated retrieval and integration of presumed relevant in-house data
Assistance in interpretation
Heuristics to extend/shrink list of genes presumed relevant
Integration with external online data
Pathways
Known relevance of genes in other diseases
Data Flow
Adapted for Agents:
Input: List of Gene IDs
Output: List of ( Gene ID Agent ID Evaluation Explanation History )
Seed of Genes
Modified List of Genes
Heuristic
Examples for Heuristics
Towards extension/shrinking of list of genes under investigation
Gene lie