Changes between Version 101 and Version 102 of MatrixProject


Ignore:
Timestamp:
Nov 7, 2012, 10:32:11 AM (9 years ago)
Author:
val_wood
Comment:

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  • MatrixProject

    v101 v102  
    1313 * etc
    1414
    15 
    16 
    17 || term ID 1 || term ID 2|| term name 2|| exceptions (everything in this column which is NOT a GO ID or "OR/AND" needs to be in brackets|| comments/checked in species ||
     15 == What is allowed in overlaps ? ==
     16
     17Annotations in intersections *always* fall into one or more the following types:
     18
     19 *  Annotation to a term which is a child of both terms i.e pentose phosphate shunt is a child of nucleotide metabolism and carbohydrate metabolism. tRNA acetylation is a child or tRNA metabolism and amino acid metabolism
     20
     21 * Indirect upstream effects
     22   * One process acts upstream of another and if the upstream process is "broken" there is an indirect downstream effect, these are usually annotated from mutant phenotypes
     23 Examples:
     24     * splicing -> cell cycle)
     25     * add more examples
     26(Note PomBase and SGD do not annotate these as bioloical processes, they are captures with "phenotype" annotations)
     27
     28 * Regulatory upstream effects
     29   Upstream signalling pathway regulating both processes
     30 Examples:
     31     * add signal transduction and transcriptional regulation examples
     32
     33 *  Multifunctional gene products, for example NOC3 appears to function in both pathways of replication and rRNA processing (note this could be an example of 2... add better examples)
     34 Examples:
     35     * urmylation pathway is involved in BOTH tRNA modification and "small mmolecule..."
     36     * add more examples
     37
     38 
     39
     40
     41 
     42
    1843
    1944Matrix tool:
     
    2146http://stove.lbl.gov:8899/cgi-bin/amigo/amigo_exp?mode=nmatrix
    2247
    23 =  Amino acid metabolism (Term 1) =
     48==  Amino acid metabolism (Term 1) ==
    2449
    2550|| term ID 1 || term ID 2|| term name 2|| exceptions (everything in this column which is NOT a GO ID or "OR/AND" needs to be in brackets|| comments/checked in species ||
     
    6893
    6994
    70 = tRNA metabolic process (Term 1) =
     95== tRNA metabolic process (Term 1) ==
    7196
    7297|| term ID 1 || term ID 2|| term name 2|| exceptions (everything in this column which is NOT a GO ID or "OR/AND" needs to be in brackets|| comments/checked in species ||