What's New In SGD in 2010?

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New Summary Paragraphs - February 8, 2010

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

REV1/YOR346W REV3/YPL167C REV7/YIL139C RPB10/YOR210W RPB11/YOL005C

RPB2/YOR151C RPB3/YIL021W RPB4/YJL140W RPB5/YBR154C RPB7/YDR404C

RPB8/YOR224C RPB9/YGL070C RPC10/YHR143W-A RPO21/YDL140C RPO26/YPR187W

RSP5/YER125W

List of Summary Paragraphs Added During the Past Week
REV1/YOR346W	REV3/YPL167C	REV7/YIL139C	RPB10/YOR210W	RPB11/YOL005C
RPB2/YOR151C	RPB3/YIL021W	RPB4/YJL140W	RPB5/YBR154C	RPB7/YDR404C
RPB8/YOR224C	RPB9/YGL070C	RPC10/YHR143W-A	RPO21/YDL140C	RPO26/YPR187W
RSP5/YER125W

GO Annotation Information - February 8, 2010

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

ADH4/YGL256W CWP1/YKL096W DAL80/YKR034W DEM1/YBR163W ECM31/YBR176W

EHD3/YDR036C FAA1/YOR317W FAA2/YER015W FAA3/YIL009W FAA4/YMR246W

FAT1/YBR041W FHL1/YPR104C FYV4/YHR059W GLR1/YPL091W GPD2/YOL059W

GRX1/YCL035C GUT1/YHL032C IMD2/YHR216W JID1/YPR061C MDL1/YLR188W

MDL2/YPL270W MNL1/YHR204W MRT4/YKL009W MZM1/YDR493W PAD1/YDR538W

RAD23/YEL037C RAD6/YGL058W REV1/YOR346W REV3/YPL167C REV7/YIL139C

ROX1/YPR065W RPP0/YLR340W SAN1/YDR143C SEC7/YDR170C TGL3/YMR313C

TGL5/YOR081C TOM71/YHR117W TRX1/YLR043C TRX2/YGR209C UBR1/YGR184C

YDC1/YPL087W YEN1/YER041W YPC1/YBR183W YVH1/YIR026C YLR281C

YLR290C YNL122C tD(GUC)Q

List of Features with GO Annotations Updated During the Past Week
ADH4/YGL256W	CWP1/YKL096W	DAL80/YKR034W	DEM1/YBR163W	ECM31/YBR176W
EHD3/YDR036C	FAA1/YOR317W	FAA2/YER015W	FAA3/YIL009W	FAA4/YMR246W
FAT1/YBR041W	FHL1/YPR104C	FYV4/YHR059W	GLR1/YPL091W	GPD2/YOL059W
GRX1/YCL035C	GUT1/YHL032C	IMD2/YHR216W	JID1/YPR061C	MDL1/YLR188W
MDL2/YPL270W	MNL1/YHR204W	MRT4/YKL009W	MZM1/YDR493W	PAD1/YDR538W
RAD23/YEL037C	RAD6/YGL058W	REV1/YOR346W	REV3/YPL167C	REV7/YIL139C
ROX1/YPR065W	RPP0/YLR340W	SAN1/YDR143C	SEC7/YDR170C	TGL3/YMR313C
TGL5/YOR081C	TOM71/YHR117W	TRX1/YLR043C	TRX2/YGR209C	UBR1/YGR184C
YDC1/YPL087W	YEN1/YER041W	YPC1/YBR183W	YVH1/YIR026C	YLR281C
YLR290C	YNL122C	tD(GUC)Q

New Summary Paragraphs - February 1, 2010

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: FKH1/YIL131C and FKH2/YNL068C .

GO Annotation Information - February 1, 2010

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

CAF4/YKR036C DNM1/YLL001W FIS1/YIL065C FKH1/YIL131C FKH2/YNL068C

MDV1/YJL112W PHO2/YDL106C PHO4/YFR034C PHO80/YOL001W PHO81/YGR233C

PHO85/YPL031C RIM8/YGL045W RPA12/YJR063W RPA135/YPR010C RPA14/YDR156W

RPA190/YOR341W RPA34/YJL148W RPA43/YOR340C RPA49/YNL248C RPC19/YNL113W

RPC40/YPR110C RRN3/YKL125W RRN5/YLR141W RRN6/YBL014C RRN7/YJL025W

RRN9/YMR270C SNC1/YAL030W STP22/YCL008C SYP1/YCR030C TGL2/YDR058C

TSA1/YML028W VAC8/YEL013W VPS1/YKR001C YPT1/YFL038C YVH1/YIR026C

List of Features with GO Annotations Updated During the Past Week
CAF4/YKR036C	DNM1/YLL001W	FIS1/YIL065C	FKH1/YIL131C	FKH2/YNL068C
MDV1/YJL112W	PHO2/YDL106C	PHO4/YFR034C	PHO80/YOL001W	PHO81/YGR233C
PHO85/YPL031C	RIM8/YGL045W	RPA12/YJR063W	RPA135/YPR010C	RPA14/YDR156W
RPA190/YOR341W	RPA34/YJL148W	RPA43/YOR340C	RPA49/YNL248C	RPC19/YNL113W
RPC40/YPR110C	RRN3/YKL125W	RRN5/YLR141W	RRN6/YBL014C	RRN7/YJL025W
RRN9/YMR270C	SNC1/YAL030W	STP22/YCL008C	SYP1/YCR030C	TGL2/YDR058C
TSA1/YML028W	VAC8/YEL013W	VPS1/YKR001C	YPT1/YFL038C	YVH1/YIR026C

SGD Quarterly Newsletter - January 29, 2010

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 Summary Paragraphs - January 25, 2010

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: ALG9/YNL219C and RAD30/YDR419W .

GO Annotation Information - January 25, 2010

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

DEM1/YBR163W FKH1/YIL131C FKH2/YNL068C HMT1/YBR034C NCR1/YPL006W

RAD30/YDR419W RPA12/YJR063W RPA135/YPR010C RPA190/YOR341W RPA34/YJL148W

RPA43/YOR340C RPA49/YNL248C RPB10/YOR210W RPB11/YOL005C RPB2/YOR151C

RPB3/YIL021W RPB5/YBR154C RPB7/YDR404C RPB8/YOR224C RPB9/YGL070C

RPC10/YHR143W-A RPC19/YNL113W RPC40/YPR110C RPO21/YDL140C RPO26/YPR187W

VAC8/YEL013W VPS74/YDR372C

List of Features with GO Annotations Updated During the Past Week
DEM1/YBR163W	FKH1/YIL131C	FKH2/YNL068C	HMT1/YBR034C	NCR1/YPL006W
RAD30/YDR419W	RPA12/YJR063W	RPA135/YPR010C	RPA190/YOR341W	RPA34/YJL148W
RPA43/YOR340C	RPA49/YNL248C	RPB10/YOR210W	RPB11/YOL005C	RPB2/YOR151C
RPB3/YIL021W	RPB5/YBR154C	RPB7/YDR404C	RPB8/YOR224C	RPB9/YGL070C
RPC10/YHR143W-A	RPC19/YNL113W	RPC40/YPR110C	RPO21/YDL140C	RPO26/YPR187W
VAC8/YEL013W	VPS74/YDR372C

New genetic interaction data file available for download from SGD - January 22, 2010

A large set of genetic interaction data from Costanzo et al., The Genetic Landscape of a Cell, Science 327: 425-431 (2010) is available for download from SGD's Download Data Files page and will be available via the web interface in the future. This study presents 74,984 genetic interactions, comprising a functional map of the cell. Thanks to the authors for providing their data to SGD.

GO Annotation Information - January 18, 2010

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

ARF3/YOR094W ATG14/YBR128C ATG16/YMR159C CSI1/YMR025W CSN9/YDR179C

DCN1/YLR128W EMI5/YOL071W GPD1/YDL022W GTS1/YGL181W LAG2/YOL025W

MLP1/YKR095W PCI8/YIL071C RPB10/YOR210W RPB11/YOL005C RPB2/YOR151C

RPB3/YIL021W RPB4/YJL140W RPB5/YBR154C RPB7/YDR404C RPB8/YOR224C

RPB9/YGL070C RPC10/YHR143W-A RPO21/YDL140C RPO26/YPR187W RRI1/YDL216C

RRI2/YOL117W YEL1/YBL060W

List of Features with GO Annotations Updated During the Past Week
ARF3/YOR094W	ATG14/YBR128C	ATG16/YMR159C	CSI1/YMR025W	CSN9/YDR179C
DCN1/YLR128W	EMI5/YOL071W	GPD1/YDL022W	GTS1/YGL181W	LAG2/YOL025W
MLP1/YKR095W	PCI8/YIL071C	RPB10/YOR210W	RPB11/YOL005C	RPB2/YOR151C
RPB3/YIL021W	RPB4/YJL140W	RPB5/YBR154C	RPB7/YDR404C	RPB8/YOR224C
RPB9/YGL070C	RPC10/YHR143W-A	RPO21/YDL140C	RPO26/YPR187W	RRI1/YDL216C
RRI2/YOL117W	YEL1/YBL060W

New Summary Paragraphs - January 11, 2010

List of Summary Paragraphs Added During the Past Week

SAR1/YPL218W SEC12/YNR026C SEC13/YLR208W SEC16/YPL085W SEC23/YPR181C

SEC24/YIL109C SEC31/YDL195W SED4/YCR067C SFB2/YNL049C SFB3/YHR098C

List of Summary Paragraphs Added During the Past Week
SAR1/YPL218W	SEC12/YNR026C	SEC13/YLR208W	SEC16/YPL085W	SEC23/YPR181C
SEC24/YIL109C	SEC31/YDL195W	SED4/YCR067C	SFB2/YNL049C	SFB3/YHR098C

GO Annotation Information - January 11, 2010

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

AIM26/YKL037W APQ12/YIL040W ARO2/YGL148W ATG1/YGL180W ATG10/YLL042C

ATG11/YPR049C ATG12/YBR217W ATG13/YPR185W ATG16/YMR159C ATG17/YLR423C

ATG2/YNL242W ATG20/YDL113C ATG21/YPL100W ATG29/YPL166W ATG3/YNR007C

ATG33/YLR356W ATG4/YNL223W ATG5/YPL149W ATG7/YHR171W ATG8/YBL078C

ATG9/YDL149W BRR6/YGL247W CAB3/YKL088W CBK1/YNL161W CIS1/YDR022C

DCI1/YOR180C FPS1/YLL043W GTS1/YGL181W ICR1 LOS1/YKL205W

MRE11/YMR224C MSN5/YDR335W PEX11/YOL147C PWR1 RAD50/YNL250W

RGT2/YDL138W SAR1/YPL218W SEC12/YNR026C SEC23/YPR181C SED4/YCR067C

SFB2/YNL049C SFB3/YHR098C SIS2/YKR072C SNF3/YDL194W SNX4/YJL036W

SSD1/YDR293C TEF1/YPR080W TEF2/YBR118W TFC1/YBR123C TFC3/YAL001C

TFC4/YGR047C TPA1/YER049W VHS3/YOR054C XRS2/YDR369C YVC1/YOR087W

ZDS1/YMR273C ZDS2/YML109W YPR146C

List of Features with GO Annotations Updated During the Past Week
AIM26/YKL037W	APQ12/YIL040W	ARO2/YGL148W	ATG1/YGL180W	ATG10/YLL042C
ATG11/YPR049C	ATG12/YBR217W	ATG13/YPR185W	ATG16/YMR159C	ATG17/YLR423C
ATG2/YNL242W	ATG20/YDL113C	ATG21/YPL100W	ATG29/YPL166W	ATG3/YNR007C
ATG33/YLR356W	ATG4/YNL223W	ATG5/YPL149W	ATG7/YHR171W	ATG8/YBL078C
ATG9/YDL149W	BRR6/YGL247W	CAB3/YKL088W	CBK1/YNL161W	CIS1/YDR022C
DCI1/YOR180C	FPS1/YLL043W	GTS1/YGL181W	ICR1	LOS1/YKL205W
MRE11/YMR224C	MSN5/YDR335W	PEX11/YOL147C	PWR1	RAD50/YNL250W
RGT2/YDL138W	SAR1/YPL218W	SEC12/YNR026C	SEC23/YPR181C	SED4/YCR067C
SFB2/YNL049C	SFB3/YHR098C	SIS2/YKR072C	SNF3/YDL194W	SNX4/YJL036W
SSD1/YDR293C	TEF1/YPR080W	TEF2/YBR118W	TFC1/YBR123C	TFC3/YAL001C
TFC4/YGR047C	TPA1/YER049W	VHS3/YOR054C	XRS2/YDR369C	YVC1/YOR087W
ZDS1/YMR273C	ZDS2/YML109W	YPR146C

Sequence and Annotation Updates - January 8, 2010

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 2010-01-04 and 2010-01-05, two new ncRNAs were annotated on Chromosome IX, the annotation of ORF DIA2/YOR080W was changed, and the sequence of Chromosome XIV was changed, affecting the annotation of ORF SAL1/YNL083W.

Changes to files available from SGD - January 8, 2010

The following changes will be made to files available for download from SGD in February 2010:
- All files available in http://downloads.yeastgenome.org/gene_registry/ will be obsoleted. This means that they will no longer be available to download.
- The annotation_change.tab file will also be obsoleted. This means this file will no longer be available to download. For information regarding ORF qualifiers (Verified, Uncharacterized, Dubious), please use the already available SGD_features.tab file. Information regarding deleted or merged chromosomal features can be found in the new deleted_merged_features.tab file (described below).
- A new file called deleted_merged_features.tab will be available from http://downloads.yeastgenome.org/chromosomal_feature/. This file will list chromosomal features that have been deleted or merged. The format of the file is identical to the annotation_change.tab file.

New Summary Paragraphs - January 4, 2010

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: HOG1/YLR113W .

GO Annotation Information - January 4, 2010

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

DCI1/YOR180C RGT2/YDL138W SNF3/YDL194W TPA1/YER049W YVC1/YOR087W