Science News

During the past week, the GO annotations have been updated for the following features:

List of Features with GO Annotations Updated During the Past Week COA4/YLR218C ERG9/YHR190W MDL1/YLR188W MDL2/YPL270W NDC1/YML031W PCP1/YGR101W

SGD is now on Facebook and Twitter! 'Like' us on Facebook or follow @yeastgenome on Twitter to get updates about new features, tips on using SGD, and interesting tidbits about yeast.

During the past week, the GO annotations have been updated for the following features:

List of Features with GO Annotations Updated During the Past Week MGS1/YNL218W OST2/YOR103C PAN2/YGL094C PGA1/YNL158W POP1/YNL221C RMP1/YLR145W SET1/YHR119W SNM1/YDR478W STV1/YMR054W TUL1/YKL034W

During the past week, the GO annotations have been updated for the following features:

List of Features with GO Annotations Updated During the Past Week ARR3/YPR201W ATG22/YCL038C EMP70/YLR083C HPA2/YPR193C MKC7/YDR144C POP1/YNL221C PTC1/YDL006W TMN2/YDR107C TMN3/YER113C YPS1/YLR120C YPS3/YLR121C YPS6/YIR039C YPS7/YDR349C ZPR1/YGR211W

During the past week, the GO annotations have been updated for the following features:

List of Features with GO Annotations Updated During the Past Week ATG34/YOL083W GAD1/YMR250W GCD10/YNL062C GCD14/YJL125C GPI8/YDR331W MYO5/YMR109W PEX8/YGR077C PUF6/YDR496C VPS60/YDR486C

During the past week, the GO annotations have been updated for the following features:

List of Features with GO Annotations Updated During the Past Week BUB3/YOR026W IPL1/YPL209C MAD1/YGL086W MAD2/YJL030W MAD3/YJL013C TOP2/YNL088W VPS60/YDR486C

Summary Paragraphs summarize published biological information for a gene/feature, and are designed to familiarize both yeast and non-yeast researchers with the general facts and important subtleties regarding a locus. During the past week, new summary paragraphs have been added to their respective Locus Summary pages for the following features: RPD3/YNL330C .

During the past week, the GO annotations have been updated for the following features:

List of Features with GO Annotations Updated During the Past Week AIM7/YDR063W CHL4/YDR254W MIP1/YOR330C NPR2/YEL062W NPR3/YHL023C PEX12/YMR026C PEX2/YJL210W RPD3/YNL330C SAP30/YMR263W SIN3/YOL004W VAC8/YEL013W

SGD sends out its quarterly newsletter to colleagues designated as contacts in SGD. An HTML version of the newsletter is available. If you would like to receive this letter in the future please use the Colleague Submission/Update form to let us know.

During the past week, the GO annotations have been updated for the following features:

List of Features with GO Annotations Updated During the Past Week 21S_RRNA/21S_rRNA ASK10/YGR097W BUB1/YGR188C CAR1/YPL111W CAR2/YLR438W CHL4/YDR254W CSM3/YMR048W CTF19/YPL018W CTF3/YLR381W CTI6/YPL181W DEP1/YAL013W EAF3/YPR023C ESA1/YOR244W FUS3/YBL016W GCN5/YGR252W GPB1/YOR371C HDA1/YNL021W HOS1/YPR068C HOS3/YPL116W IML3/YBR107C MCM16/YPR046W MCM21/YDR318W MCM22/YJR135C PHO23/YNL097C RCO1/YMR075W REC8/YPR007C RGC1/YPR115W RPD3/YNL330C RPN11/YFR004W RPN12/YFR052W RXT2/YBR095C RXT3/YDL076C SAP30/YMR263W SDS3/YIL084C SET2/YJL168C SGO1/YOR073W SIN3/YOL004W SPO13/YHR014W STE11/YLR362W STE4/YOR212W STE5/YDR103W STE7/YDL159W UBP6/YFR010W UME1/YPL139C UME6/YDR207C

Please take our brief survey to let us know how you use SGD. The information you provide will help us prepare for our grant renewal this fall.

Links to two new resources have been added to SGD: 1) GeneMANIA, a biological network integration for gene prioritization and functional prediction, and 2) the Complexome Database, a database of consensus protein complex predictions. Links to both resources have been added to the "Interactions" pull-down menu on the Locus Summary page, and to the "Interaction Resources" sections at the bottom of the Protein and Interaction pages. See Warde-Farley, et al. Nucleic Acids Res. 2010 for more information on GeneMANIA, and Benschop, et al. Molecular Cell 2010 for more information on Complexome. Thanks to Quaid Morris and Sylva Donaldson for help in setting up the GeneMANIA links and to Patrick Kemmeren for helping set up the Complexome links.

During the past week, the GO annotations have been updated for the following features:

List of Features with GO Annotations Updated During the Past Week BUD27/YFL023W CDC45/YLR103C CDC50/YCR094W CDC7/YDL017W CHL4/YDR254W CTF4/YPR135W DPB11/YJL090C ETP1/YHL010C GOS1/YHL031C ILV3/YJR016C IML3/YBR107C MAM1/YER106W MCM10/YIL150C MCM2/YBL023C MCM3/YEL032W MCM4/YPR019W MCM5/YLR274W MCM6/YGL201C MCM7/YBR202W PSF1/YDR013W PSF2/YJL072C PSF3/YOL146W SEC20/YDR498C SED5/YLR026C SFT1/YKL006C-A SGO1/YOR073W SLD2/YKL108W SLD3/YGL113W SLD5/YDR489W STE7/YDL159W TAH11/YJR046W VNX1/YNL321W YKT6/YKL196C

Summary Paragraphs summarize published biological information for a gene/feature, and are designed to familiarize both yeast and non-yeast researchers with the general facts and important subtleties regarding a locus. During the past week, new summary paragraphs have been added to their respective Locus Summary pages for the following features:

List of Summary Paragraphs Added During the Past Week PRE1/YER012W PRE10/YOR362C PRE2/YPR103W PRE3/YJL001W PRE4/YFR050C PRE5/YMR314W PRE6/YOL038W PRE7/YBL041W PRE8/YML092C PRE9/YGR135W PUP1/YOR157C PUP2/YGR253C PUP3/YER094C SCL1/YGL011C

During the past week, the GO annotations have been updated for the following features:

List of Features with GO Annotations Updated During the Past Week BET1/YIL004C BOS1/YLR078C CKA1/YIL035C CKB1/YGL019W CKB2/YOR039W FSP2/YJL221C GPX1/YKL026C GYP7/YDL234C IMA1/YGR287C IMA2/YOL157C IMA3/YIL172C IMA5/YJL216C KTR1/YOR099W KTR3/YBR205W MAG1/YER142C MSY1/YPL097W NAT3/YPR131C OSM1/YJR051W PRB1/YEL060C SEC22/YLR268W SED5/YLR026C STE6/YKL209C UFE1/YOR075W USE1/YGL098W YEL047C

Summary Paragraphs summarize published biological information for a gene/feature, and are designed to familiarize both yeast and non-yeast researchers with the general facts and important subtleties regarding a locus. During the past week, new summary paragraphs have been added to their respective Locus Summary pages for the following features: TOF1/YNL273W .

During the past week, the GO annotations have been updated for the following features:

List of Features with GO Annotations Updated During the Past Week ACT1/YFL039C ADE8/YDR408C AFG1/YEL052W AFT2/YPL202C AHP1/YLR109W ALO1/YML086C ARG4/YHR018C ARH1/YDR376W ASK10/YGR097W ATX1/YNL259C CCP1/YKR066C DOT5/YIL010W EOS1/YNL080C ERG11/YHR007C ERG24/YNL280C ERG3/YLR056W ERG4/YGL012W ERG5/YMR015C ERG9/YHR190W ERV1/YGR029W FAP7/YDL166C FSP2/YJL221C GAD1/YMR250W GCY1/YOR120W GIS1/YDR096W GLR1/YPL091W GND1/YHR183W GPX1/YKL026C GPX2/YBR244W GRE3/YHR104W GRX1/YCL035C GRX2/YDR513W GRX3/YDR098C GRX4/YER174C GRX5/YPL059W GSG1/YDR108W HSP12/YFL014W HYR1/YIR037W IGO1/YNL157W IGO2/YHR132W-A IMA1/YGR287C IMA2/YOL157C IMA3/YIL172C IMA5/YJL216C LOT6/YLR011W LTV1/YKL143W LYS1/YIR034C LYS20/YDL182W LYS21/YDL131W MAL11/YGR289C MAL12/YGR292W MAL23 MAL32/YBR299W MCR1/YKL150W MET2/YNL277W MPR1 MSN2/YMR037C MSN4/YKL062W MXR1/YER042W MXR2/YCL033C NCE103/YNL036W NGR1/YBR212W NPR2/YEL062W OCA1/YNL099C OXR1/YPL196W OYE2/YHR179W OYE3/YPL171C PEP3/YLR148W POS5/YPL188W PRE1/YER012W PRE10/YOR362C PRE2/YPR103W PRE3/YJL001W PRE4/YFR050C PRE5/YMR314W PRE6/YOL038W PRE7/YBL041W PRE8/YML092C PRE9/YGR135W PRX1/YBL064C PUP1/YOR157C PUP2/YGR253C PUP3/YER094C RCK2/YLR248W SCL1/YGL011C SIT4/YDL047W SKN7/YHR206W SRX1/YKL086W SVF1/YDR346C THR1/YHR025W TIM18/YOR297C TMA19/YKL056C TRR1/YDR353W TRR2/YHR106W TRX1/YLR043C TRX2/YGR209C TRX3/YCR083W TSA1/YML028W TSA2/YDR453C UBA4/YHR111W UGA2/YBR006W URM1/YIL008W YAH1/YPL252C YAR1/YPL239W YBP1/YBR216C YEF3/YLR249W YJU3/YKL094W YPR1/YDR368W YPT1/YFL038C ZTA1/YBR046C YBL055C YDL124W YJR096W YKL069W

Try the beta version of YeastMine for flexible queries and fast retrieval of chromosomal features, sequences, and GO-related annotations using predefined template queries or customized queries. New datatypes and additional templates will be added in the upcoming months. YeastMine is part of a joint project with Intermine, the Rat Genome Database (RGD), and The Zebrafish Model Organism Database (ZFIN) to provide interoperability between the model organism databases via shared datatypes, such as Gene Ontology (GO) annotations or orthologs. Be a beta tester and email us your comments and questions about YeastMine.

The Gene Ontology Consortium has recently changed the format of the GO annotations file (gene_associations file, GAF) to version 2.0. The files contain two new columns (17 columns total): the Annotation Extension column and the Gene Product Form ID column. Details of format 2.0 are available at: GAF 2.0. SGD has updated the S. cerevisiae GAF to format 2.0 on its FTP site. Although SGD has not populated the two new columns with data, gene_associations file parsers/scripts could be affected by the format change.

Summary Paragraphs summarize published biological information for a gene/feature, and are designed to familiarize both yeast and non-yeast researchers with the general facts and important subtleties regarding a locus. During the past week, new summary paragraphs have been added to their respective Locus Summary pages for the following features: ADE4/YMR300C .