SGD News

New Papers - May 6, 2008

During the past week, 60 new papers have been added to SGD.

New Summary Paragraphs - May 6, 2008

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: DDP1/YOR163W and PLC1/YPL268W .

GO Annotation Information - May 6, 2008

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
BTT1/YDR252W	CMC1/YKL137W	GAL1/YBR020W	GAL10/YBR019C	GAL7/YBR018C
GCY1/YOR120W	GET3/YDL100C	GRE3/YHR104W	PAU5/YFL020C	PET127/YOR017W
PRS1/YKL181W	PRS2/YER099C	PRS3/YHL011C	PRS4/YBL068W	PRS5/YOL061W
RRP15/YPR143W	SAE2/YGL175C	SNR7-L/snR7-L	SNR7-S/snR7-S	SPT6/YGR116W
VPS55/YJR044C	VPS68/YOL129W	YPR1/YDR368W	YDL124W	YJR096W

SGD Quarterly Newsletter - April 30, 2008

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.

New Gene Ontology (GO) Evidence Codes - April 29, 2008

The Gene Ontology Consortium (GOC) has added three new subcodes for the ISS (Inferred from Sequence or Structural Similarity) evidence code in order to distinguish the types of sequence-based methods used as evidence in making annotations: Inferred from Sequence Alignment (ISA), Inferred from Sequence Orthology (ISO), and Inferred from Sequence Model (ISM). Full documentation on these evidence codes is available at the GOC website. SGD has started using these new subcodes to annotate S. cerevisiae gene products as of April 16th, and these evidence codes are included on the Locus Summary pages, the GO Annotation details and references pages, the downloadable gene_association.sgd file and the GO Term Finder tool.

New Summary Paragraphs - April 29, 2008

List of Summary Paragraphs Added During the Past Week
ATG1/YGL180W	ATG10/YLL042C	ATG11/YPR049C	ATG12/YBR217W	ATG13/YPR185W
ATG14/YBR128C	ATG15/YCR068W	ATG16/YMR159C	ATG17/YLR423C	ATG18/YFR021W
ATG19/YOL082W	ATG2/YNL242W	ATG20/YDL113C	ATG21/YPL100W	ATG22/YCL038C
ATG23/YLR431C	ATG26/YLR189C	ATG27/YJL178C	ATG29/YPL166W	ATG3/YNR007C
ATG4/YNL223W	ATG5/YPL149W	ATG7/YHR171W	ATG8/YBL078C	ATG9/YDL149W
CIS1/YDR022C	SNX4/YJL036W	VPS30/YPL120W

GO Annotation Information - April 29, 2008

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
CWH43/YCR017C	IST1/YNL265C	MBA1/YBR185C	MRS6/YOR370C	NTH2/YBR001C
OXA1/YER154W	ROM1/YGR070W	ROM2/YLR371W	SLC1/YDL052C	TRM3/YDL112W
TRM44/YPL030W	TRM9/YML014W

GO Annotation Information - April 22, 2008

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
AAC3/YBR085W	AAH1/YNL141W	AFI1/YOR129C	ARF3/YOR094W	BIO7/YHR214W-G
BIO8/YHR214W-F	CDC28/YBR160W	DHH1/YDL160C	ERP3/YDL018C	ERP4/YOR016C
ERP5/YHR110W	ERP6/YGL002W	GSF2/YML048W	GTR1/YML121W	GTR2/YGR163W
HUB1/YNR032C-A	INO80/YGL150C	IRS4/YKR019C	IVY1/YDR229W	KHS1
MAL62	NAT5/YOR253W	NUS1/YDL193W	PGA1/YNL158W	PGA2/YNL149C
PGA3/YML125C	PHO86/YJL117W	PHS1/YJL097W	PMR1/YGL167C	SEC39/YLR440C
SNR13/snR13	SNR35/snR35	SNR39B/snR39B	SNR40/snR40	SNR41/snR41
SNR47/snR47	SNR48/snR48	SNR50/snR50	SNR51/snR51	SNR52/snR52
SNR53/snR53	SNR54/snR54	SNR55/snR55	SNR56/snR56	SNR57/snR57
SNR58/snR58	SNR59/snR59	SNR6/snR6	SNR60/snR60	SNR61/snR61
SNR62/snR62	SNR63/snR63	SNR64/snR64	SNR65/snR65	SNR66/snR66
SNR67/snR67	SNR68/snR68	SNR69/snR69	SNR70/snR70	SNR71/snR71
SNR72/snR72	SNR73/snR73	SNR74/snR74	SNR75/snR75	SNR76/snR76
SNR77/snR77	SNR78/snR78	SNR79/snR79	SNR80/snR80	SNR81/snR81
SNR82/snR82	SNR83/snR83	SNR84/snR84	SNR85/snR85	SYT1/YPR095C
TAH1/YCR060W	TAX4/YJL083W	TRM44/YPL030W	XDJ1/YLR090W	YEL1/YBL060W

New Wiki Tab - April 18, 2008

In order to increase accessibility to SGD's Community Wiki, a new Wiki tab has been added to the set of navigation tabs found at the top of the following pages: Locus Summary, Locus History, Literature Guide, Gene Ontology evidence and references, Phenotype details and references, Interaction details and references, Expression Summary, and Protein Info. These Wiki tabs point to the locus-specific pages in the SGD Wiki. We invite researchers to edit the wiki pages for their favorite gene(s).

GO Annotation Information - April 15, 2008

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
ARC15/YIL062C	ARP2/YDL029W	CDC31/YOR257W	CSR1/YLR380W	DIP2/YLR129W
EDC3/YEL015W	EMG1/YLR186W	FAS1/YKL182W	FLD1/YLR404W	FRA1/YLL029W
FRA2/YGL220W	GRX6/YDL010W	GRX7/YBR014C	GTR1/YML121W	GTS1/YGL181W
HCS1/YKL017C	LSM4/YER112W	MPS3/YJL019W	PET54/YGR222W	PKP1/YIL042C
PKP2/YGL059W	PRP18/YGR006W	PRP8/YHR165C	PWP2/YCR057C	RPB4/YJL140W
RTM1	SNR7-L/snR7-L	SNR7-S/snR7-S	UTP13/YLR222C	UTP18/YJL069C
UTP21/YLR409C	UTP6/YDR449C	VPS4/YPR173C

New Summary Paragraphs - April 8, 2008

GO Annotation Information - April 8, 2008

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
ATP25/YMR098C	BFR2/YDR299W	BMS1/YPL217C	BUD21/YOR078W	CBF5/YLR175W
CIN2/YPL241C	DBP8/YHR169W	DIM1/YPL266W	DIP2/YLR129W	ECM16/YMR128W
EMG1/YLR186W	ENP1/YBR247C	ENP2/YGR145W	ENS2	FRA1/YLL029W
FRA2/YGL220W	GIC2/YDR309C	GRX3/YDR098C	HAS1/YMR290C	IMP3/YHR148W
IMP4/YNL075W	KRE33/YNL132W	KRR1/YCL059C	LSR1	MAL11/YGR289C
MAL41	MAL61	MPP10/YJR002W	MPR1	MRD1/YPR112C
NAN1/YPL126W	NHP6A/YPR052C	NHP6B/YBR089C-A	NOC4/YPR144C	NOP1/YDL014W
NOP14/YDL148C	NOP58/YOR310C	NRK1/YNL129W	PNO1/YOR145C	PNP1/YLR209C
POB3/YML069W	PRP43/YGL120C	PRS1/YKL181W	RCL1/YOL010W	RDN37-1
RDN37-2	RNR1/YER070W	RNR2/YJL026W	RNR3/YIL066C	RNR4/YGR180C
ROK1/YGL171W	RRP12/YPL012W	RRP5/YMR229C	RRP9/YPR137W	SCL1/YGL011C
SIK1/YLR197W	SMI1/YGR229C	SNR19/snR19	SNR7-L/snR7-L	SNR7-S/snR7-S
SOF1/YLL011W	SPP382/YLR424W	SPT16/YGL207W	SSC1/YJR045C	TFB5/YDR079C-A
TSA1/YML028W	TSA2/YDR453C	TSR1/YDL060W	UBP8/YMR223W	UTP10/YJL109C
UTP13/YLR222C	UTP15/YMR093W	UTP18/YJL069C	UTP20/YBL004W	UTP21/YLR409C
UTP22/YGR090W	UTP30/YKR060W	UTP4/YDR324C	UTP6/YDR449C	UTP7/YER082C
UTP8/YGR128C	UTP9/YHR196W	YLR003C

Post job opportunities through SGD - April 2, 2008

Periodically SGD is asked to advertise job opportunities. In response, we have created a page in the Community Wiki to allow researchers to post positions available in their labs. This page is linked from the Career Resources page listed in the navigation menu. These pages can be edited by clicking the "edit" tab at the top of the page.

GO Annotation Information - April 1, 2008

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
ARO10/YDR380W	BNA1/YJR025C	BNA2/YJR078W	BNA4/YBL098W	BNA5/YLR231C
BNA6/YFR047C	BNI1/YNL271C	BSC2/YDR275W	DDI2/YFL061W	FLD1/YLR404W
FMP48/YGR052W	FMP52/YER004W	HSP31/YDR533C	LPD1/YFL018C	LRC4/YMR098C
MYO4/YAL029C	NAT2/YGR147C	NRK1/YNL129W	PDH1/YPR002W	PHM8/YER037W
PHO12/YHR215W	RNR4/YGR180C	ROG3/YFR022W	RPB7/YDR404C	SHE2/YKL130C
SHE3/YBR130C	SHE4/YOR035C	SIT4/YDL047W	STP4/YDL048C	TMN3/YER113C
UBC12/YLR306W	UBC9/YDL064W	VPS4/YPR173C	YRO2/YBR054W	YBL112C
YCL049C	YDR222W	YEL075C	YER130C	YER158C
YFL065C	YFL066C	YFL067W	YFL068W	YFR026C
YGL242C	YGR146C	YHL044W	YJL016W	YKR075C
YLR297W	YML002W	YML119W	YMR144W	YNR068C
YPR157W

New Summary Paragraphs - March 25, 2008

GO Annotation Information - March 25, 2008

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
ATG22/YCL038C	BUD23/YCR047C	CBR1/YIL043C	CCR4/YAL021C	CRN1/YLR429W
CYB2/YML054C	CYC1/YJR048W	CYC7/YEL039C	DID2/YKR035W-A	DUN1/YDL101C
EEB1/YPL095C	EHT1/YBR177C	FBP1/YLR377C	INN1/YNL152W	KRR1/YCL059C
LPD1/YFL018C	MOT3/YMR070W	NAT2/YGR147C	PKP1/YIL042C	PKP2/YGL059W
PTC5/YOR090C	PTC6/YCR079W	PTC7/YHR076W	RAD54/YGL163C	RDH54/YBR073W
RFX1/YLR176C	ROX1/YPR065W	RPS14A/YCR031C	RPS14B/YJL191W	RPS2/YGL123W
RPS6A/YPL090C	RPS6B/YBR181C	RPS7A/YOR096W	RPS7B/YNL096C	RPS9A/YPL081W
RPS9B/YBR189W	SNR35/snR35	UTP21/YLR409C	UTP22/YGR090W	VPS4/YPR173C
WTM1/YOR230W	WTM2/YOR229W	YMR210W

New Summary Paragraphs - March 18, 2008

List of Summary Paragraphs Added During the Past Week
ADH1/YOL086C	ADH2/YMR303C	ADH3/YMR083W	ADH4/YGL256W	ADH5/YBR145W
ALG7/YBR243C	SFA1/YDL168W

GO Annotation Information - March 18, 2008

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
ADH1/YOL086C	ADH2/YMR303C	ADH3/YMR083W	ADH4/YGL256W	ADH5/YBR145W
ARO10/YDR380W	BNA1/YJR025C	BNA2/YJR078W	BNA6/YFR047C	EAF3/YPR023C
IRC11/YOR013W	IRC14/YOR135C	IRC15/YPL017C	IRC16/YPR038W	IRC19/YLL033W
IRC4/YDR540C	IRC5/YFR038W	IRC7/YFR055W	IRC8/YJL051W	IRC9/YJL142C
PDC1/YLR044C	PDC5/YLR134W	PDC6/YGR087C	RAD54/YGL163C	RDH54/YBR073W
RNR4/YGR180C	SFA1/YDL168W	SKY1/YMR216C	SPT6/YGR116W	THI3/YDL080C
TPO1/YLL028W	TRS120/YDR407C	TRS130/YMR218C

New Summary Paragraphs - March 11, 2008

List of Summary Paragraphs Added During the Past Week
BNA1/YJR025C	BNA2/YJR078W	BNA4/YBL098W	BNA5/YLR231C	BNA6/YFR047C
BNA7/YDR428C	CRN1/YLR429W	NMA1/YLR328W	NMA2/YGR010W	NPT1/YOR209C
NRK1/YNL129W	PNC1/YGL037C	PNP1/YLR209C	QNS1/YHR074W	SIR2/YDL042C
URH1/YDR400W

GO Annotation Information - March 11, 2008

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
ADH1/YOL086C	BNA3/YJL060W	DMA1/YHR115C	DMA2/YNL116W	DPB2/YPR175W
DPB3/YBR278W	DPB4/YDR121W	GRE2/YOL151W	IRC25/YLR021W	IST2/YBR086C
LPD1/YFL018C	MIP1/YOR330C	MST27/YGL051W	MST28/YAR033W	NAR1/YNL240C
NRK1/YNL129W	POC4/YPL144W	POL1/YNL102W	POL12/YBL035C	POL2/YNL262W
POL3/YDL102W	POL31/YJR006W	POL32/YJR043C	POL4/YCR014C	PRM8/YGL053W
PRM9/YAR031W	RAD28/YDR030C	RAD30/YDR419W	REV3/YPL167C	REV7/YIL139C
RPB7/YDR404C	SLK19/YOR195W	SLX5/YDL013W	SOD1/YJR104C	SOD2/YHR008C
TPO1/YLL028W	ULS1/YOR191W	YAR029W	YGR031W	YHL044W
YMR210W

GO annotations with IEAs now in SGD's gene_association file - March 10, 2008

SGD has changed the contents of our file that contains GO annotations. This is a major change as it now includes annotations that are associated with computationally predicted methods. These annotations include computationally predicted annotations to the Gene Ontology created by the Gene Ontology Annotation (GOA) project at EBI, Hinxton UK. The file available from the GO Consortium is called gene_association.sgd

Sequence and Annotation Updates - March 7, 2008

SGD curators periodically update the systematic sequence and its annotation. Information regarding changes can be found via the Summary of Chromosome Sequence and Annotation Updates and in the "Locus History" pages of affected features. Files on the SGD FTP site are updated weekly.

Between 2008-3-3 and 2008-3-7, the sequence of Chromosome I was updated, affecting GCV3/YAL044C; and the annotation of the LTR YCRCtau1 on Chromosome III was updated.

New Summary Paragraphs - March 4, 2008

GO Annotation Information - March 4, 2008

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
ADH1/YOL086C	CRN1/YLR429W	DLD3/YEL071W	GRE2/YOL151W	GUP1/YGL084C
IRC15/YPL017C	LAS17/YOR181W	LGE1/YPL055C	LIA1/YJR070C	MMS22/YLR320W
MYO3/YKL129C	MYO5/YMR109W	NBA1/YOL070C	PAN1/YIR006C	PCL1/YNL289W
PCL10/YGL134W	PCL2/YDL127W	PCL5/YHR071W	PCL7/YIL050W	PCL8/YPL219W
PCL9/YDL179W	PHO80/YOL001W	PHO85/YPL031C	RMD11/YHL023C	RMR1/YGL250W
RPC25/YKL144C	SEC27/YGL137W	SEC28/YIL076W	SOH1/YGL127C	STE14/YDR410C

Potential downtime at SGD - February 28, 2008

SGD may be temporarily unavailable without notice due to an air conditioning problem in our machine room. We will try to keep SGD online. However, it is likely that some SGD pages may be unavailable until this is repaired. You can also view basic yeast data at the SGD Lite database. We apologize in advance for any inconvenience this may cause.

GO Annotation Information - February 26, 2008

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
ACF2/YLR144C	ADH4/YGL256W	ECM7/YLR443W	ENT3/YJR125C	ENT5/YDR153C
HNM1/YGL077C	ICP55/YER078C	KEG1/YFR042W	KRE6/YPR159W	MPT5/YGL178W
NUD1/YOR373W	OLA1/YBR025C	RAD54/YGL163C	RDH54/YBR073W	SCS2/YER120W
SIM1/YIL123W	STE14/YDR410C	TPO1/YLL028W	TPO2/YGR138C	TPO3/YPR156C
TPO4/YOR273C	YCR023C	YGR031W

New Summary Paragraphs - February 19, 2008

List of Summary Paragraphs Added During the Past Week
SOL1/YNR034W	SOL2/YCR073W-A	SOL3/YHR163W	SOL4/YGR248W	UGA4/YDL210W

GO Annotation Information - February 19, 2008

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
ATE1/YGL017W	BNA3/YJL060W	BNA6/YFR047C	DBP1/YPL119C	GCV2/YMR189W
HIR1/YBL008W	HIR2/YOR038C	HIR3/YJR140C	HPC2/YBR215W	HXK1/YFR053C
ICT1/YLR099C	MTD1/YKR080W	MTF1/YMR228W	NAM7/YMR080C	NFS1/YCL017C
NIF3/YGL221C	NRT1/YOR071C	PDS1/YDR113C	RAD3/YER171W	RAD54/YGL163C
RDH54/YBR073W	RFX1/YLR176C	RPO41/YFL036W	SIM1/YIL123W	SLY1/YDR189W
SSL2/YIL143C	THI7/YLR237W	THI72/YOR192C	UGA4/YDL210W

Coming Soon: GO annotations with IEAs to be added to SGD's gene_association file on March 8th - February 14, 2008

On March 8, 2008, SGD will change the contents of our files that contains GO annotations. This is a major change as we will add annotations that are associated with computationally predicted methods. The SGD file currently does not include annotations that are made using the IEA evidence code. These annotations include computationally predicted annotations to the Gene Ontology created by the Gene Ontology Annotation (GOA) project at EBI, Hinxton UK. The file available from the GO Consortium is called gene_association.sgd.

New Summary Paragraphs - February 12, 2008

List of Summary Paragraphs Added During the Past Week
AQR1/YNL065W	ATG1/YGL180W	ATG12/YBR217W	ATG18/YFR021W	ATG21/YPL100W
ATG3/YNR007C	ATG5/YPL149W	ATG7/YHR171W	ATG8/YBL078C	DTR1/YBR180W
FLR1/YBR008C	HOL1/YNR055C	HRD1/YOL013C	QDR1/YIL120W	QDR2/YIL121W
QDR3/YBR043C	SSM4/YIL030C	TPO1/YLL028W	TPO2/YGR138C	TPO3/YPR156C
TPO4/YOR273C	VPS30/YPL120W	YHK8/YHR048W

GO Annotation Information - February 12, 2008

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
AGP3/YFL055W	ALR2/YFL050C	ARG82/YDR173C	ASC1/YMR116C	ASF1/YJL115W
ASN1/YPR145W	ASN2/YGR124W	BEM4/YPL161C	BNA3/YJL060W	BNA7/YDR428C
BRE1/YDL074C	BUD27/YFL023W	CDC48/YDL126C	CDC73/YLR418C	CKB2/YOR039W
CLN2/YPL256C	CSE2/YNR010W	CUE1/YMR264W	CWC24/YLR323C	DER1/YBR201W
EAF3/YPR023C	ELF1/YKL160W	ELG1/YOR144C	HHT1/YBR010W	HNM1/YGL077C
HRD1/YOL013C	HRD3/YLR207W	IPK1/YDR315C	KAR2/YJL034W	KCS1/YDR017C
LEO1/YOR123C	MMS1/YPR164W	MMS22/YLR320W	NPL4/YBR170C	PAF1/YBR279W
PBS2/YJL128C	RPD3/YNL330C	RTF1/YGL244W	RTT10/YPL183C	RTT101/YJL047C
RTT103/YDR289C	RTT105/YER104W	RTT106/YNL206C	RTT107/YHR154W	RTT109/YLL002W
SCS7/YMR272C	SIC1/YLR079W	SIN3/YOL004W	SNR128/snR128	SNR13/snR13
SNR18/snR18	SNR24/snR24	SNR35/snR35	SNR38/snR38	SNR39/snR39
SNR39B/snR39B	SNR40/snR40	SNR41/snR41	SNR47/snR47	SNR48/snR48
SNR50/snR50	SNR51/snR51	SNR52/snR52	SNR53/snR53	SNR54/snR54
SNR55/snR55	SNR56/snR56	SNR57/snR57	SNR58/snR58	SNR59/snR59
SNR60/snR60	SNR61/snR61	SNR62/snR62	SNR63/snR63	SNR64/snR64
SNR65/snR65	SNR66/snR66	SNR67/snR67	SNR68/snR68	SNR69/snR69
SNR70/snR70	SNR71/snR71	SNR72/snR72	SNR73/snR73	SNR74/snR74
SNR75/snR75	SNR76/snR76	SNR77/snR77	SNR78/snR78	SNR79/snR79
SNR80/snR80	SNR81/snR81	SNR82/snR82	SNR83/snR83	SNR84/snR84
SNR85/snR85	SNR87/snR87	SNR9/snR9	SOH1/YGL127C	SPT21/YMR179W
SPT5/YML010W	SRB5/YGR104C	SSK2/YNR031C	SSK22/YCR073C	SSM4/YIL030C
THI71/YOR071C	UBX2/YML013W	UFD1/YGR048W	USA1/YML029W	YFH7/YFR007W
YOS9/YDR057W

SGD RSS Feed - February 12, 2008

Updates and announcements from SGD are now available via our RSS feed. To read it, you will need to subscribe to our RSS feed using an RSS news reader. Applications that can read our RSS feed include FeedDemon, Firefox, Safari, Mac Mail version 3.1, and Google Reader.

SGD Quarterly Newsletter - January 31, 2008

Update on Yeast Biochemical Pathways - January 29, 2008

All 133 pathways available from the Yeast Biochemical Pathways have been manually reviewed and referenced. In addition, pathways that have not been documented to occur in yeast have been removed. Curation of pathways unique to S. cerevisiae is ongoing, and we welcome feedback from the research community.

The yeast biochemical pathways data are available from SGD's FTP site in two files: the biochemical_pathways.tab file and yeastcyc11.0.tar.200801.gz. These files are updated monthly. In addition, for easy download and accessibility, the yeastcyc11.0 data files are also available for download through the Pathways PGDB Registry for use with the Pathway Tools software.

2008 NAR Database Article - January 8, 2008

The 2008 Nucleic Acids Research Database issue is now available. This issue includes a paper (HTML | PDF) by the SGD staff describing the annotation methods used to assign GO annotations at SGD.