Changes between Version 1 and Version 2 of PombeGeneLosses


Ignore:
Timestamp:
Oct 3, 2014, 1:55:20 PM (6 years ago)
Author:
vw253
Comment:

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  • PombeGeneLosses

    v1 v2  
    11
    22
    3 == Known pombe gene losses ==
    4 
    5 === Lipid metabolic process (mainly fatty acid oxidation?) ===
     3 == Known pombe gene losses ==
     4
     5 === Lipid metabolic process (mainly fatty acid oxidation?) ===
    66 
    77  * YAT1 YAR035W carnitine O-acetyltransferase (human, CPT2)
     
    2828 
    2929
    30 === TMA (translation machinery associated) ===
     30 === TMA (translation machinery associated) ===
    3131
    3232  * TMA64 YDR117C (human LGTN)
     
    3636
    3737
    38  === nucleobase containing small molecule met  ===
     38 === Nucleobase containing small molecule met  ===
    3939
    4040  * YBR140C (from Compara)
     
    6969  * CYS4 YGR155W cystathionine beta-synthase (human CBS)
    7070
    71   ==== urea metabolism ====
     71  ==== Urea metabolism ====
    7272
    7373  * YBR208C (from Compara)
     
    8484  * YPR026W (from Compara)
    8585
    86 === subset of carbohydrate , Glycogen metabolism ===
     86 === Subset of carbohydrate , Glycogen metabolism ===
    8787
    8888  * GLC3 YEL011W glycogen branching enzyme (human GBE1)
     
    9595 
    9696
    97  === Transmembrane Transporters ===
     97  === Transmembrane Transporters ===
    9898
    9999  * FUN26 YAL022C (human SLC29A1,2,3,4)
     
    119119 
    120120
    121  ===  transcription and chromatin remodelleing complexes CHRAC and isw1-2 complexes ===
     121  ===  transcription and chromatin remodelleing complexes CHRAC and isw1-2 complexes ===
    122122
    123123  * ITC1  YGL133W CHRAC complex isw1-a  complex (human BAZ1A,B) (no compara)
     
    139139  * YPL177C (from Compara)
    140140
    141  == chromosome organization ==
     141  == Chromosome organization ==
    142142  * ISW1 YBR245C isw1-a/b  complex amily  confirmed by compara (FP?)
    143143  * ISW2  YOR304W CHRAC complex family  confirmed by compara (FP?)
     
    145145  * HOS1 YPR068C (from Compara)
    146146
    147   === nucleocytoplsmic transport  ===
     147  === Nucleocytoplsmic transport  ===
    148148
    149149  * YKL068W (from Compara) (checked)
     
    160160  * YPL164C (from Compara)
    161161
    162  === repair ===
     162  === DNA repair ===
    163163
    164164  * YFL007W this isn't repair, cant figure why its mapping here
     
    168168  * OGG1 YML060W "CBF3 complex"  base excision repair protein (human OGG1)
    169169
    170   === replication ===
     170  === DNA replication ===
    171171 
    172172  * YDL101C (from Compara)
    173173 
    174  === mitotoic cell cycle regulation=== (does not map here)
     174 === Miitotoic cell cycle regulation === (does not map here)
    175175 
    176176  * YPR120C (from Compara)
     
    182182  * RNY1  YPL123C (no compara)
    183183
    184   ===  meotic cell cycle -===
     184  ===  Meiotic cell cycle -===
    185185 
    186186  * YIL112W (from Compara)  check classification
    187187 
    188188 
    189   === signalling ===
     189  === Signalling ===
    190190
    191191  * YBR164C (from Compara)
     
    201201  * PDE2 YOR360C high affinity 3',5'-cAMP phosphodiesterase (family has human members, but no pombe member http://pfam.xfam.org/family/PF00233?type=Family#tabview=tab7)
    202202 
    203  === Mitochondrial ===
     203  === Mitochondrial organization ===
    204204
    205205  * COX23 YHR116w http://www.pantherdb.org/panther/family.do?clsAccession=PTHR13626 (has human) (no compara)
    206206  * TOM6 YOR045W  this paper links budding yeast to human, no pombe yet http://www.ncbi.nlm.nih.gov/pubmed/18331822 (no compara)
    207207
    208   === proteases ===
     208  === Proteases ===
    209209
    210210  * YCR045C (from Compara) (REMOVE?)
    211211 
    212  === proteasome assembly ===
     212  === Proteasome assembly ===
    213213
    214214  * YGL004C (from Compara)
    215215
    216   === misc ===
     216  === Misc ===
     217 
    217218  move to above (in list)
    218219  * YPC1 YBR183W paralog YDC1 (conserved in human ACER3) (no compara)
     
    221222  * KXD1 YGL079W BLOC-1 complex (conserved in human KXD1)
    222223  * SNN1 YNL086W  BLOC-1 complex (conserved in human SNAPIN & BLOC1S6)
     224 
    223225  === Unknown process ===
    224226 
    225  * AML1  YGR001C adenine methyltransferase, has human, (conserved in human  N6AMT2) http://pfam.xfam.org/family/PF10237?type=Family#tabview=tab7
     227  * AML1  YGR001C adenine methyltransferase, has human, (conserved in human  N6AMT2) http://pfam.xfam.org/family/PF10237?type=Family#tabview=tab7
    226228 
    227229  === Compara false positive ===