1 / 6

Theoretical methods for predicting gene function III. Predicting protein function

Theoretical methods for predicting gene function III. Predicting protein function by genomic context Inspired by: Huynen et al. (2000), Genome research 10,1204-1210 Predicting Protein Function by Genomic Context: Qualitative Evaluation and Quantitative Inferences. S. Wodak, ULB

sherri
Download Presentation

Theoretical methods for predicting gene function III. Predicting protein function

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript


  1. Theoretical methods for predicting gene function III. Predicting protein function by genomic context Inspired by: Huynen et al. (2000), Genome research 10,1204-1210 Predicting Protein Function by Genomic Context: Qualitative Evaluation and Quantitative Inferences S. Wodak, ULB Inter-university DEA/DES in Bioinformatics

  2. [4] Use information on genome context Gene order; co-regulation Pathway/process reconstruction 1-Gene fusion/fission analysis 2-Conservation of the local genomic context (in different genomes) -as neighbours -in runs (genes with the same direction of translation, separated by fewer than 300 bases) 3-Similar patterns of gene co-occurence in different genomes phylogenic profiles 4-Metabolic reconstruction

  3. Domain swapping 1-Gene fusion/fission analysis Marcotte et al., (1999) Scence, 285, 751-753 Enright et al. (1999) Nature, 402, 86-90 Proteins from genes whose homologs are fused (especially if they are orthologs of the fused genes) tend to have a related function... Protein Interactions ?? Human Succinyl Co-A-transferase E. coli acetate Co-A-transferase a E. coli acetate Co-A-transferase b

  4. 2-Conservation of the local genomic context (in different genomes) deoB : Phosphoribomutase Pmm : phosphomannomutases, phosphoglucomutases Generally genomic context provides information on the process in which a gene is involved

  5. 3- Phylogenic profiles Similar patterns of gene co-occurrence in different genomes Pellegrini et al. (1999) SC p2 p1 p2 p7 p3 p4 p5 p5 Phylogenic profile p6 EC SC BS HI p1 1 0 1 p2 1 1 0 p3 0 1 1 p4 1 0 0 p5 1 1 1 p6 0 1 1 p7 1 1 0 p3 p1 p7 p1 p2 p3 p4 p6 p5 p6 p7 p5 BS EC HI p2 & p7 are functionally linked p3 & p6 are functionally linked

  6. 2-Conservation of the local genomic context (in different genomes) 5th gene is missing Nucleoside salvage pathway deoB ? deoD deoC deoA cdd pmm M. genitalium deoD pmm M. tuberculosis deoB : Phosphoribomutase Pmm : phosphomannomutases, phosphoglucomutases Generally genomic context provides information on the process in which a gene is involved

More Related