Changes between Version 181 and Version 182 of MatrixProject


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Timestamp:
Jan 4, 2013, 4:44:43 PM (9 years ago)
Author:
val_wood
Comment:

--

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  • MatrixProject

    v181 v182  
    4646http://stove.lbl.gov:8899/cgi-bin/amigo/amigo_exp?mode=nmatrix
    4747
    48 with GO slim list (template list at the bottom of this page)
    49 
     48with GO slim list (template list at the bottom of this page
     49
     50(Note that the tables must use the syntax described in the column headers for parsing)
    5051
    5152==  Amino acid metabolism (Term 1) ==
    5253
    53 || 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 ||
     54|| term ID 1 || term ID 2|| term name 2|| exceptions  format: GO: xxxxxxx OR GO:xxxxxxx (and free text in single set of parentheses) || checked in species S.p; etc {comments in curly brackets} ||
     55
    5456||GO:0006520||GO:0006310|| DNA recombination || NO OVERLAP || S.p; M.m; S.c. ||
    5557||GO:0006520||GO:0006281|| DNA repair || GO:0006521 OR GO:0006338 (regulation of cellular amino acid metabolic process -NOTE transcriptional OR chromatin remodelling- NOTE, this may be indirect for repair???) ||S.p; M.m; S.c.||
     
    122124== tRNA metabolic process (Term 1) ==
    123125
    124 || 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 ||
     126
     127|| term ID 1 || term ID 2|| term name 2|| exceptions  format: GO: xxxxxxx OR GO:xxxxxxx (and free text in single set of parentheses) || checked in species S.p; etc {comments in curly brackets} ||
     128
     129
    125130||GO:0006399||GO:0006310|| DNA recombination || NO OVERLAP||S.p.; M.m||
    126131||GO:0006399||GO:0006281|| DNA repair|| NO OVERLAP||S.p.; M.m.||
     
    172177== translation (Term 1) ==
    173178
    174 || 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 ||
     179
     180|| term ID 1 || term ID 2|| term name 2|| exceptions  format: GO: xxxxxxx OR GO:xxxxxxx (and free text in single set of parentheses) || checked in species S.p; etc {comments in curly brackets} ||
     181
    175182
    176183||GO:0006412||GO:0006310|| DNA recombination || GO:0000018 OR GO:0006417   (regulation of translation OR regulation of DNA recombination)  ||S.p.; M.m {2 ISO's from human to fix}; S.c||
     
    222229== ribosome biogenesis (Term 1) ==
    223230
    224 || 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 ||
     231
     232|| term ID 1 || term ID 2|| term name 2|| exceptions  format: GO: xxxxxxx OR GO:xxxxxxx (and free text in single set of parentheses) || checked in species S.p; etc {comments in curly brackets} ||
     233
    225234||GO:0042254||GO:0006310|| DNA recombination || NO OVERLAP  ||S.p.; S.c; M.m {after isotype switching fix, actually this might be OK....}||
    226235||GO:0042254||GO:0006281|| DNA repair || LOTS cerevisiae ||S.p.||
     
    267276
    268277== transmembrane transport (Term 1) ==
    269 
    270 || 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 ||
     278|| term ID 1 || term ID 2|| term name 2|| exceptions  format: GO: xxxxxxx OR GO:xxxxxxx (and free text in single set of parentheses) || checked in species S.p; etc {comments in curly brackets} ||
    271279
    272280||GO:0055085||GO:0006310|| DNA recombination || NO OVERLAP ||S.p.; S.c; M.m||
     
    315323== vitamin metabolic process (Term 1) ==
    316324
    317 || 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 ||
     325
     326
     327|| term ID 1 || term ID 2|| term name 2|| exceptions  format: GO: xxxxxxx OR GO:xxxxxxx (and free text in single set of parentheses) || checked in species S.p; etc {comments in curly brackets} ||
    318328
    319329||GO:0006766||GO:0006310|| DNA recombination || NO OVERLAP ||S.p.; S.c; M.m {1, looks dodgy ifn2 same paper as snai2 below}||
     
    363373== regulation of mitotic cell cycle (Term 1) ==
    364374
    365 || 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 ||
    366 
     375|| term ID 1 || term ID 2|| term name 2|| exceptions  format: GO: xxxxxxx OR GO:xxxxxxx (and free text in single set of parentheses) || checked in species S.p; etc {comments in curly brackets} ||
    367376
    368377||GO:0007346 || GO:0006310 || DNA recombination || - ||-||
     
    413422== DNA repair (Term 1) ==
    414423
    415 || 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 ||
    416 
     424
     425|| term ID 1 || term ID 2|| term name 2|| exceptions  format: GO: xxxxxxx OR GO:xxxxxxx (and free text in single set of parentheses) || checked in species S.p; etc {comments in curly brackets} ||
    417426
    418427||GO:0006281|| GO:0006310 || DNA recombination || - ||-||
     
    461470== DNA replication (Term 1) ==
    462471
    463 || 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 ||
    464 
     472
     473|| term ID 1 || term ID 2|| term name 2|| exceptions  format: GO: xxxxxxx OR GO:xxxxxxx (and free text in single set of parentheses) || checked in species S.p; etc {comments in curly brackets} ||
    465474
    466475||GO:0006260 || GO:0006310 || DNA recombination || - ||-||
     
    511520
    512521
    513 ||GO:0006310 || DNA recombination || - ||-||
    514 ||GO:0006281 || DNA repair || - ||-||
    515 ||GO:0006260 || DNA replication || - ||-||
    516 ||GO:0030437 || ascospore formation || - ||-||
    517 ||GO:0005975 || carbohydrate metabolic process || - ||-||
    518 ||GO:0007155 || cell adhesion || - ||-||
    519 ||GO:0006520 || cellular amino acid metabolic process || - ||-||
    520 ||GO:0070882 || cellular cell wall organization or biogenesis || - ||-||
    521 ||GO:0016568 || chromatin modification || - ||-||
    522 ||GO:0051276 || chromosome organization  || - ||-||
    523 ||GO:0007059 || chromosome segregation || - ||-||
    524 ||GO:0051186 || cofactor metabolic process  || - ||-||
    525 ||GO:0000747 || conjugation with cellular fusion  || - ||-||
    526 ||GO:0000910 || cytokinesis || - ||-||
    527 ||GO:0002181 || cytoplasmic translation  || - ||-||
    528 ||GO:0007010 || cytoskeleton organization  || - ||-||
    529 ||GO:0007163 || establishment or maintenance of cell polarity  || - ||-||
    530 ||GO:0006091 || generation of precursor metabolites and energy  || - ||-||
    531 ||GO:0006629 || lipid metabolic process  || - ||-||
    532 ||GO:0016071 || mRNA metabolic process  || - ||-||
    533 ||GO:0007126 || meiosis  || -||-||
    534 ||GO:0007005 || mitochondrion organization  || - ||-||
    535 ||GO:0071941 || nitrogen cycle metabolic process  || - ||-||
    536 ||GO:0055086 || nucleobase-containing small molecule metabolic process  || - ||-||
    537 ||GO:0006913 || nucleocytoplasmic transport  || - ||-||
    538 ||GO:0007031 || peroxisome organization  || - ||-||
    539 ||GO:0030163 || protein catabolic process  || - ||-||
    540 ||GO:0006461 || protein complex assembly  || - ||-||
    541 ||GO:0006457 || protein folding  || - ||-||
    542 ||GO:0006486 || protein glycosylation  || - ||-||
    543 ||GO:0051604 || protein maturation  || - ||-||
    544 ||GO:0070647 || protein modification by small protein conjugation or removal  || - ||-||
    545 ||GO:0006605 || protein targeting  || - ||-||
    546 ||GO:0007346 || regulation of mitotic cell cycle  || - ||-||
    547 ||GO:0042254 || ribosome biogenesis  || - ||-||
    548 ||GO:0023052 || signaling  || - ||-||
    549 ||GO:0006399 || tRNA metabolic process  || - ||-||
    550 ||GO:0006351 || transcription, DNA-dependent  || - ||-||
    551 ||GO:0055085 || transmembrane transport  || - ||-||
    552 ||GO:0007033 || vacuole organization  || - ||-||
    553 ||GO:0016192 || vesicle-mediated transport  || - ||-||
    554 ||GO:0006766 || vitamin metabolic process  || - ||-||
     522||GO:0006310|| DNA recombination || - ||-||
     523||GO:0006281|| DNA repair || - ||-||
     524||GO:0006260|| DNA replication || - ||-||
     525||GO:0030437|| ascospore formation || - ||-||
     526||GO:0005975|| carbohydrate metabolic process || - ||-||
     527||GO:0007155|| cell adhesion || - ||-||
     528||GO:0006520|| cellular amino acid metabolic process || - ||-||
     529||GO:0070882|| cellular cell wall organization or biogenesis || - ||-||
     530||GO:0016568|| chromatin modification || - ||-||
     531||GO:0051276|| chromosome organization  || - ||-||
     532||GO:0007059|| chromosome segregation || - ||-||
     533||GO:0051186|| cofactor metabolic process  || - ||-||
     534||GO:0000747|| conjugation with cellular fusion  || - ||-||
     535||GO:0000910|| cytokinesis || - ||-||
     536||GO:0002181|| cytoplasmic translation  || - ||-||
     537||GO:0007010|| cytoskeleton organization  || - ||-||
     538||GO:0007163|| establishment or maintenance of cell polarity  || - ||-||
     539||GO:0006091|| generation of precursor metabolites and energy  || - ||-||
     540||GO:0006629|| lipid metabolic process  || - ||-||
     541||GO:0016071|| mRNA metabolic process  || - ||-||
     542||GO:0007126|| meiosis  || -||-||
     543||GO:0007005|| mitochondrion organization  || - ||-||
     544||GO:0071941|| nitrogen cycle metabolic process  || - ||-||
     545||GO:0055086|| nucleobase-containing small molecule metabolic process  || - ||-||
     546||GO:0006913|| nucleocytoplasmic transport  || - ||-||
     547||GO:0007031|| peroxisome organization  || - ||-||
     548||GO:0030163|| protein catabolic process  || - ||-||
     549||GO:0006461|| protein complex assembly  || - ||-||
     550||GO:0006457|| protein folding  || - ||-||
     551||GO:0006486|| protein glycosylation  || - ||-||
     552||GO:0051604|| protein maturation  || - ||-||
     553||GO:0070647|| protein modification by small protein conjugation or removal  || - ||-||
     554||GO:0006605|| protein targeting  || - ||-||
     555||GO:0007346|| regulation of mitotic cell cycle  || - ||-||
     556||GO:0042254|| ribosome biogenesis  || - ||-||
     557||GO:0023052|| signaling  || - ||-||
     558||GO:0006399|| tRNA metabolic process  || - ||-||
     559||GO:0006351|| transcription, DNA-dependent  || - ||-||
     560||GO:0055085|| transmembrane transport  || - ||-||
     561||GO:0007033|| vacuole organization  || - ||-||
     562||GO:0016192|| vesicle-mediated transport  || - ||-||
     563||GO:0006766|| vitamin metabolic process  || - ||-||
    555564
    556565Template to type into Matrix
     
    597606GO:0016192
    598607GO:0006766
     608
     609to get rules
     610 cat annotation_matrix_rules.rtf  |grep -v MOUSE  | grep -v LATER | grep -v "SEE ABOVE" | grep -v LOTS | grep "GO:" | perl -pi -e 's/\(.*\)//g' | perl -pi -e 's/\|\|/,/g' | cut -f 2,3,5 -d ,
     611
     612