READING LIST: GO Annotation Camp

June 1-4, 2005
Stanford University
Stanford, CA

Recommended Reading for GO Annotation Camp 2005

Page Contents

Basics about GO
Two papers for large group working session
List of all papers

Key to Recommended Reading

   strongly recommended

   also useful

   more information

   selected for small working groups

   additional papers

Basics about GO

If you are completely new to GO, we recommend that you read a little about it before arriving at the Annotation Camp.

The Gene Ontology Consortium. 2000. Gene Ontology: tool for the unification of biology. Nat Genet 25: 25-29. [ABSTRACT] [PDF]

The Gene Ontology Consortium. 2001. Creating the gene ontology resource: design and implementation. Genome Res 11: 1425-1433. [ABSTRACT] [FULL TEXT]

The Gene Ontology Consortium. 2004. The Gene Ontology (GO) database and informatics resource. Nucleic Acids Res 32: D258-D261. [ABSTRACT] [FULL TEXT]

A more extensive reading list of publications about GO or using GO is available from the Gene Ontology Bibliography page.

Two papers for large group working session

During the large group working session on Wednesday June 1st, we will read two papers and discuss the GO annotations that may or may not, be reasonably made from each paper. We request that you read these papers at least once before arriving at the camp.

Chang M, Bellaoui M, Zhang C, Desai R, Morozov P, Delgado-Cruzata L, Rothstein R, Freyer GA, Boone C, Brown GW (2005) RMI1/NCE4, a suppressor of genome instability, encodes a member of the RecQ helicase/Topo III complex. EMBO J [PDF]
supplementary material for Chang et al.

the before ontology file
the after ontology file

Loyola A, Huang JY, LeRoy G, Hu S, Wang YH, Donnelly RJ, Lane WS, Lee SC, Reinberg D. (2003) Functional analysis of the subunits of the chromatin assembly factor RSF. Mol Cell Biol. 23(19):6759-68. [PDF]

We will also have a brief presentation of a good example of a common pitfall. The paper is listed here in case you want to take a look at it in advance.

Appelbaum L, Anzulovich A, Baler R, Gothilf Y. Homeobox-clock protein interaction in zebrafish. A shared mechanism for pineal-specific and circadian gene expression. J Biol Chem. 2005 Mar 25; 280(12):11544-51. [PDF]

Papers selected by the group

During working sessions on Thursday and Friday, we will divide into small groups and deal with a number of different papers. As a consistency exercise, some of the groups will deal independently with the same paper. We will record each groups' annotations and compare. Not all of the papers can be dealt with by the small group working sessions, but we will leave the last working session on Friday for individual work. This will be an opportunity to work on any of the papers not used in the previous working sessions, or on other papers that highlight questions you have.

Download Excel worksheet for recording annotations

Papers for Small Group Discussion

Paper number Submitter Broad category Common name Scientific name Links Submitted comment

1 Gwinn Bacteria (pathogen: human) flu Haemophilus influenzae Rd PDF    Abstract "This paper uses a combination of sequence similarity, expression pattern and mutant phenotype to describe several genes. Process pretty clear, function/component - not much info."

2 Pilcher Microorganism Slime mold Dictystelium discoideum PDF    Abstract paper describing novel gene with no conserved functional domains; involved in O-glycosylation; several potential processes but no function or component

3 Drabkin Multicellular animal Mouse Mus musculus PDF    Abstract Paper on one mouse marker; straightforward.

4 Huntley Plant Mustard weed Arabidopsis thaliana PDF    Abstract "This paper describes characterization of an isoform of Arabidopsis Villin, several experiments demonstrate it's involvement in actin filament binding, organization and depolymerization."

5 Berardini Plant Mustard weed Arabidopsis thaliana PDF    Abstract "Selected this paper because annotation was very straightforward, uses evidence codes IDA, IGI and TAS in the process"

6 Collins Multicellular animal Fruitfly Drosophila melanogaster PDF    Abstract Straight forward paper about a protein involved in Hh movement with a vairety of different kinds of data requiring different evidence codes.

7A Collmer Bacteria (pathogen: plant) bacterial speck Pseudomonas syringae pv tomato PDF    Abstract Paper about a virulence factor in a plant pathogenic bacterium that induces plant susceptibility by inhibiting host programmed cell death (PCD). Good for annotating both pathogen virulence factors and host defense responses.

7B Topalis Insect vector Anopheles gambiae PDF    Abstract "A ""typical"" microarray-based survey showing genes going up and down upon infection and correlation to distinct phenotypes. This is a two-organism process, how does one deal with this?"

8A Tripathy & Master Pathogen (plant) Oomycete Phytophthora sojae PDF    Abstract "Necrosis inducing protein from Phytophthora sojae was identified and was found to be responsible for the colonization of host tissues during necrotrophic phase of growth. Similar sequences in other pathogen were compared with P.sojae, but P.sojae protein was found to be much more powerful inducer of necrosis than other organisms."

"A paper describing a nonenzymatic protein that is pathogenic to plants. This protein exemplifies those that have been characterized by what they elicite in other hosts, and is therefore changing for function annotations."

8B Purkayastha Virus Hepatitis E PDF    Abstract Provides evidence for the role ORF3 in enhancing {alpha}_1 m export from the hepatocyte.

9A D'Eustachio Two organisms S. cerevisiae & H. sapiens PDF    Abstract "Human gene restores viability in mutant yeast strain, providing how much evidence for normal function of the human gene in humans, the yeast gene in yeasts, and for the conservation of a single molecular_function between the two species? (Reactome uses this paper to assign a definitive human molecular_function to PIG-N.)"

9B Sakaniwa Plant Rice PDF    Abstract How to add GO to the gene which mRNA will be processed by alternative splicing.

10A Elsik Multicellular animal Honey bee Apis mellifera PDF    Abstract paper providing annotation for gene involved with mulitple functions including innate immunity and vitellogenesis

10B Smith Multicellular animal Rat Rattus PDF    Abstract A straightforward paper about the cloning and characterization of rat GCRP. Cellular component changes between inactivated and activated states.

11A Hance Fungi Yeast Saccharomyces cerevisiae PDF    Abstract Combining both GO and protein-protein interaction data in the prediction of protein function for unknown proteins.

11B Sese Multicellular animal Fruitfly Drosophila melanogaster PDF    Abstract association study between mutations in EGFR region and their wing shapes

12A Zheng Fungi Yeast PDF    Abstract "A paper that involves cellular compoent, biological process and molecular function"

12B Howe Multicellular animal zebrafish Danio rerio PDF    Abstract "Authors use knockdown approach to show redundant roles for wnt3a, wnt8 and sp5l in somitogenesis, mesoderm development, notochord development, tail development, etc. The annotations make use of IMP and IGI evidence and show how a full related set of annotations captures the essence of what the paper shows."

13 Stover Microorganism Ciliate Tetrahymena thermophila PDF    Abstract "This phylogenetic analysis the only paper about T. thermophila enolase. It shows beyond a doubt that this is an enolase gene, but mentions nowhere in the text what enolase typically does or where it can be found in the cell."

14 Khodiyar Multicellular animal Human Homo sapiens PDF    Abstract "Uses a range of experimental procedures, and provides info on several genes."

15 Mao Bacteria (symbiont: plant) Rhizobia Sinorhizobium meliloti PDF    Abstract The paper used microarray analysis and enzyme assay to annotate katA and Smc01944 genes involved in oxidative stress response

16 Bastiani Multicellular animal Worm Caenorhabditis elegans PDF    Abstract "I chose this paper because it features a wide array of approaches to characterize mutant phenotypes. In our group, this led to confusion regarding evidence code usage (since assays were done on mutants, I think IMP is appropriate; some curators were tempted to use IDA for electrophysiological assays on mutants). Annotations can also be made to all three GO categories (CC via IDA, MF via ISS, and BP via IMP)."

17 Huntley Plant Mustard weed Arabidopsis thaliana PDF    Abstract "This paper attempts to describe the genetic interactions between five HD-ZIP genes involved in meristem function through mutant analysis. It describes new alleles, processes and expression patterns for these genes."

18 Foulger Multicellular animal Human Homo sapiens PDF    Abstract A query whether an **indirect** interaction with a complex is sufficient data to support a 'colocalizes_with X complex' component annotation.

Additional Papers

Balakrishnan Fungi Yeast Saccharomyces cerevisiae PDF    Abstract In this paper the authors report the identification of all the proteins in the yeast mitochondrial genome using a combination of techniques like MassSpec and Gel electrophoresis. This is a large scale study and provides component annotations for about 700 yeast gene products which could be bulk loaded.

Bastiani Multicellular animal Worm Caenorhabditis elegans PDF    Abstract "I chose this paper because it's a little tricky to annotate with respect to cellular component. It requires careful reading of the Supplementary Materials section, and then I believe that only one protein can be annotated to cellular component because the specificity of the other antibodies used was not determined. This is a common problem when annotating C. elegans papers. One annotation can be made to a protein complex (small nuclear ribonucleoprotein complex) via ISS. In addition, biological process data can also be extracted from this paper using the IGI evidence codes (based on RNAi of multiple genes), and I thought it would be good to go over how to do this."

Berardini Plant Mustard weed Arabidopsis thaliana PDF    Abstract Selected this paper because annotating the genes in it required new GO terms that did not exist.

Cherepanov Virus Vaccinia PDF    Abstract Initial characterization of the product of vaccinia virus A28L gene. Localization and function.

Cherepanov Virus Variola PDF    Abstract A review on two Variola proteins involved in immunoregulatory functions. Smallpox inhibitor of complement enzymes (SPICE) and Chemokine binding protein type-II (CKBP-II).

Collins Multicellular animal Fruitfly Drosophila melanogaster PDF    Abstract A paper about the extracellular movement of Hh and Wg that presents data that likely requires the addition of new terms to GO.

Collmer Bacteria (pathogen: plant) bacterial speck Pseudomonas syringae pv tomato PDF    Abstract "Paper identifying and characterizing bacterial biosynthetic genes for the phytotoxin coronatine, shown to have a role in plant pathogenesis."

D'Eustachio Multicellular animal Human Homo sapiens PDF    Abstract How to get a GO molecular_function term more specific than GO:0004867 serine-type endopeptidase inhibitor activity to describe C1Inh protein?

Drabkin Multicellular animal Mouse Mus musculus PDF    Abstract Several types of evidence codes are used in this paper; multiple markers can be annotated.

Elsik Multicellular animal Honey bee Apis mellifera PDF    Abstract paper providing annotation for gene involved in neuromodulation

Fey Microorganism Slime mold Dictystelium discoideum PDF    Abstract paper characterizing novel alpha kinase with one or two not so straight forward annotations.

Fey Microorganism Slime mold Dictystelium discoideum PDF    Abstract "very typical, complex, Dictyostelium signal transduction paper"

Gwinn Bacteria (useful) "Superbug, resistant to radiation" Deinococcus radiodurans PDF    Abstract This paper is a straightforward characterization of an enzyme's activity.

Hance Fungi Yeast Saccharomyces cerevisiae PDF    Abstract Combining both GO and protein-protein interaction data in the prediction of protein function for unknown proteins.

Heiges Parasite apicomplexan coccidian parasite Cryptosporidum PDF    Abstract This is a comparison of Cryptosporidium and Plasmodium. An example of the need for gene ontology comparisons among species of the same phylum where the cellular machinery and life-cycle stages significantly differ. The plasmodium community has been active in updating GO definitions to cover apicomplexans; are the definitions sufficient to cover cryptosporidium?

Heiges Parasite apicomplexan coccidian parasite Cryptosporidum PDF    Abstract Cryptosporidium has acquired a large number of genes from distant phylogenetic sources (algal and eubacterial). An example of the need to make genome comparisons with unrelated species?

Hood Fungi Neurospora crassa PDF    Abstract This paper provides annotations for two genes that allow for efficient homologous recombination in Neurospora.

Hood Fungi Neurospora crassa PDF    Abstract This study identified a G(gamma) protein in Neurospora and characterizes its function and interaction with other G protein subunits.

Howe Multicellular animal zebrafish Danio rerio PDF    Abstract "Authors report first characterization of the zebrafish robo4 gene and use antisense techniques to characterizes the role of this gene product in angiogenesis. This is a fairly straightforward paper, demonstrating IMP evidence with a clear choice of GO terms."

Huntley Plant Mustard weed Arabidopsis thaliana PDF    Abstract "This paper describes characterization of an isoform of Arabidopsis Villin, several experiments demonstrate it's involvement in actin filament binding, organization and depolymerization."

Joshi Bacteria (symbiont: plant) nitrogen-fixing symbiont of soybean Bradyrhizobium japonicum PDF    Abstract paper provides complete denitrification pathway of bacterium B.japonicum

Joshi Plant Rice Oryza sativa PDF    Abstract paper mentions isolation and characterization of abiotic stress-inducible dehydrin gene in Rice

Karalius Plant Tomato Lycopersicon esculentum PDF    Abstract Annotation for QTL involved in tomato brix

Khodiyar Multicellular animal Human Homo sapiens PDF    Abstract "Cross species expts, how do we annotate these?"

Louis Insect vector Anopheles gambiae PDF    Abstract "A paper demonstrating a new role for annexin, again involving two organisms. Now what?"

Louis Multicellular animal Mosquito Anopheles gambiae PDF    Abstract "A straightforward paper but known genes are assigned to several processes. Under which conditions GO terms become obsolete or new ones are added or old ones changed, etc? "

Lu Multicellular animal "Mouse, rat" PDF    Abstract A paper about function domain of rectifying K channels

Lu Multicellular animal Mouse PDF    Abstract A paper on cloning of a K-dependent Na/Ca exchanger protein

Mao Bacteria (symbiont: plant) Rhizobia Sinorhizobium meliloti PDF    Abstract The paper used mutant analysis to annotate phbB and phbC genes involved in exopolysaccharide synthesis

Master Fungi P. chrysosporium PDF    Abstract A paper describing the secretome of a fungus grown on cellulose. Enzyme annotations described in this paper are commonly used in our Fungal Genome Project.

Morris PDF    Abstract EXTRACELLULAR (SECRETED PROTEINS APPEAR TO BE AN IMPORTANT PART OF THE REORTOIRE OF PLANT PATHOGENS.

Morris PDF    Abstract Avirulence genes(Avr) and the corresponding resistance genes(Rps) in their host form the basis of the interaction that results in race specific resistance of plants against pplant pathogens.

Mueller Plant Tomato & pathogen Solanum lycopersicum PDF    Abstract A paper about interaction of pathogen proteins with tomato proteins. I'm not sure how such interactions between proteins from different organisms are annotated in GO.

Mueller Plant Tomato Solanum lycopersicum PDF    Abstract Paper about a tomato fruit ripening gene rin.

Pilcher Microorganism Slime mold Dictystelium discoideum PDF    Abstract paper invesigating kinesin family protein required for cytokinesis; several possible processes and components

Purkayastha Bacteria (pathogen: animal) Q-fever pathogen Coxiella burnetii PDF    Abstract Experimental evidence suggests that acid phosphatase activity is a major virulence determinant in C. burnetii.

Sakaniwa Plant Rice PDF    Abstract Abnormal expression strategy.

Sese Fungi Yeast Saccharomyces cerevisiae PDF    Abstract "introductory paper for morphological database and its data-mining functions on the web, which also contains some examples to reveal gene functions"

Singh Plant Mustard weed Arabidopsis thaliana PDF    Abstract Identification of a gene responsible for enhanced pollen tube growth

Singh Plant Rice PDF    Abstract Gene involved in root cell shape

Smith Multicellular animal Rat Rattus PDF    Abstract An older paper about cloning of rat alcohol dehydrogenases which raises a question about how granular the biological process term should be.

Stover Microorganism Ciliate Tetrahymena thermophila PDF    Abstract "The authors present a number of hypotheses about the function of this distant Drosophila HP1 homolog, based on its cellular localization and sequence motifs. A typical paper in my field."

Tanaka Plant Rice Oryza sativa PDF    Abstract rice chromosome1 paper from our Institute (Natl. Inst. Agrobiol. Sci.) (I would like to introduce the activity of our Institute)

Tanaka Plant Mustard weed Arabidopsis thaliana PDF    Abstract "paper reporting the BZR1 gene functioning as a member of plant signaling pathway mediated by the plant hormones, Brassinosteroids (I would like to introduce an example of plant unique characteristics)"

Topalis Multicellular animal Mosquito Anopheles gambiae PDF    Abstract "A straightforward paper describing many Odorant binding proteins in mosquitoes. All involved in olfaction, but is this the same biological process? Think of why some people are attractive to mossies and some not. "

Tripathy Pathogen (plant) Oomycete Phytophthora sojae PDF    Abstract Avr1b-1 and Avr1b-2 are required for establishing infection in soybean and are closely located in the pathogen genome.

Van Slyke Multicellular animal Zebrafish Danio rerio PDF    Abstract straitforward not too many genes.

Yamasaki Multicellular animal Human Homo sapiens PDF    Abstract paper of annotation of human transcripts based on gene ontology

Yamasaki Multicellular animal Human Homo sapiens PDF    Abstract GOAL: automated Gene Ontology analysis of expression profiles

Yu Multicellular animal Human Homo sapiens PDF    Abstract This study utilized mRNA differential display and the Gene Ontology (GO) analysis to characterize the multiple interactions of a number of genes with gene expression profile involved in squamous cell cervical carcinoma.

Yu Multicellular animal Frog Xenopus laevis PDF    Abstract applying multiple Support Vector Machines (SVM) for developing a large-scale annotation system.

Papers for Small Group Discussion
Paper number	Submitter	Broad category	Common name	Scientific name	Links	Submitted comment
1	Gwinn	Bacteria (pathogen: human)	flu	Haemophilus influenzae Rd	PDF Abstract	"This paper uses a combination of sequence similarity, expression pattern and mutant phenotype to describe several genes. Process pretty clear, function/component - not much info."
2	Pilcher	Microorganism	Slime mold	Dictystelium discoideum	PDF Abstract	paper describing novel gene with no conserved functional domains; involved in O-glycosylation; several potential processes but no function or component
3	Drabkin	Multicellular animal	Mouse	Mus musculus	PDF Abstract	Paper on one mouse marker; straightforward.
4	Huntley	Plant	Mustard weed	Arabidopsis thaliana	PDF Abstract	"This paper describes characterization of an isoform of Arabidopsis Villin, several experiments demonstrate it's involvement in actin filament binding, organization and depolymerization."
5	Berardini	Plant	Mustard weed	Arabidopsis thaliana	PDF Abstract	"Selected this paper because annotation was very straightforward, uses evidence codes IDA, IGI and TAS in the process"
6	Collins	Multicellular animal	Fruitfly	Drosophila melanogaster	PDF Abstract	Straight forward paper about a protein involved in Hh movement with a vairety of different kinds of data requiring different evidence codes.
7A	Collmer	Bacteria (pathogen: plant)	bacterial speck	Pseudomonas syringae pv tomato	PDF Abstract	Paper about a virulence factor in a plant pathogenic bacterium that induces plant susceptibility by inhibiting host programmed cell death (PCD). Good for annotating both pathogen virulence factors and host defense responses.
7B	Topalis	Insect vector		Anopheles gambiae	PDF Abstract	"A ""typical"" microarray-based survey showing genes going up and down upon infection and correlation to distinct phenotypes. This is a two-organism process, how does one deal with this?"
8A	Tripathy & Master	Pathogen (plant)	Oomycete	Phytophthora sojae	PDF Abstract	"Necrosis inducing protein from Phytophthora sojae was identified and was found to be responsible for the colonization of host tissues during necrotrophic phase of growth. Similar sequences in other pathogen were compared with P.sojae, but P.sojae protein was found to be much more powerful inducer of necrosis than other organisms." "A paper describing a nonenzymatic protein that is pathogenic to plants. This protein exemplifies those that have been characterized by what they elicite in other hosts, and is therefore changing for function annotations."
8B	Purkayastha	Virus	Hepatitis E		PDF Abstract	Provides evidence for the role ORF3 in enhancing {alpha}_1 m export from the hepatocyte.
9A	D'Eustachio	Two organisms		S. cerevisiae & H. sapiens	PDF Abstract	"Human gene restores viability in mutant yeast strain, providing how much evidence for normal function of the human gene in humans, the yeast gene in yeasts, and for the conservation of a single molecular_function between the two species? (Reactome uses this paper to assign a definitive human molecular_function to PIG-N.)"
9B	Sakaniwa	Plant	Rice		PDF Abstract	How to add GO to the gene which mRNA will be processed by alternative splicing.
10A	Elsik	Multicellular animal	Honey bee	Apis mellifera	PDF Abstract	paper providing annotation for gene involved with mulitple functions including innate immunity and vitellogenesis
10B	Smith	Multicellular animal	Rat	Rattus	PDF Abstract	A straightforward paper about the cloning and characterization of rat GCRP. Cellular component changes between inactivated and activated states.
11A	Hance	Fungi	Yeast	Saccharomyces cerevisiae	PDF Abstract	Combining both GO and protein-protein interaction data in the prediction of protein function for unknown proteins.
11B	Sese	Multicellular animal	Fruitfly	Drosophila melanogaster	PDF Abstract	association study between mutations in EGFR region and their wing shapes
12A	Zheng	Fungi	Yeast		PDF Abstract	"A paper that involves cellular compoent, biological process and molecular function"
12B	Howe	Multicellular animal	zebrafish	Danio rerio	PDF Abstract	"Authors use knockdown approach to show redundant roles for wnt3a, wnt8 and sp5l in somitogenesis, mesoderm development, notochord development, tail development, etc. The annotations make use of IMP and IGI evidence and show how a full related set of annotations captures the essence of what the paper shows."
13	Stover	Microorganism	Ciliate	Tetrahymena thermophila	PDF Abstract	"This phylogenetic analysis the only paper about T. thermophila enolase. It shows beyond a doubt that this is an enolase gene, but mentions nowhere in the text what enolase typically does or where it can be found in the cell."
14	Khodiyar	Multicellular animal	Human	Homo sapiens	PDF Abstract	"Uses a range of experimental procedures, and provides info on several genes."
15	Mao	Bacteria (symbiont: plant)	Rhizobia	Sinorhizobium meliloti	PDF Abstract	The paper used microarray analysis and enzyme assay to annotate katA and Smc01944 genes involved in oxidative stress response
16	Bastiani	Multicellular animal	Worm	Caenorhabditis elegans	PDF Abstract	"I chose this paper because it features a wide array of approaches to characterize mutant phenotypes. In our group, this led to confusion regarding evidence code usage (since assays were done on mutants, I think IMP is appropriate; some curators were tempted to use IDA for electrophysiological assays on mutants). Annotations can also be made to all three GO categories (CC via IDA, MF via ISS, and BP via IMP)."
17	Huntley	Plant	Mustard weed	Arabidopsis thaliana	PDF Abstract	"This paper attempts to describe the genetic interactions between five HD-ZIP genes involved in meristem function through mutant analysis. It describes new alleles, processes and expression patterns for these genes."
18	Foulger	Multicellular animal	Human	Homo sapiens	PDF Abstract	A query whether an indirect interaction with a complex is sufficient data to support a 'colocalizes_with X complex' component annotation.

Additional Papers
	Balakrishnan	Fungi	Yeast	Saccharomyces cerevisiae	PDF Abstract	In this paper the authors report the identification of all the proteins in the yeast mitochondrial genome using a combination of techniques like MassSpec and Gel electrophoresis. This is a large scale study and provides component annotations for about 700 yeast gene products which could be bulk loaded.
	Bastiani	Multicellular animal	Worm	Caenorhabditis elegans	PDF Abstract	"I chose this paper because it's a little tricky to annotate with respect to cellular component. It requires careful reading of the Supplementary Materials section, and then I believe that only one protein can be annotated to cellular component because the specificity of the other antibodies used was not determined. This is a common problem when annotating C. elegans papers. One annotation can be made to a protein complex (small nuclear ribonucleoprotein complex) via ISS. In addition, biological process data can also be extracted from this paper using the IGI evidence codes (based on RNAi of multiple genes), and I thought it would be good to go over how to do this."
	Berardini	Plant	Mustard weed	Arabidopsis thaliana	PDF Abstract	Selected this paper because annotating the genes in it required new GO terms that did not exist.
	Cherepanov	Virus	Vaccinia		PDF Abstract	Initial characterization of the product of vaccinia virus A28L gene. Localization and function.
	Cherepanov	Virus	Variola		PDF Abstract	A review on two Variola proteins involved in immunoregulatory functions. Smallpox inhibitor of complement enzymes (SPICE) and Chemokine binding protein type-II (CKBP-II).
	Collins	Multicellular animal	Fruitfly	Drosophila melanogaster	PDF Abstract	A paper about the extracellular movement of Hh and Wg that presents data that likely requires the addition of new terms to GO.
	Collmer	Bacteria (pathogen: plant)	bacterial speck	Pseudomonas syringae pv tomato	PDF Abstract	"Paper identifying and characterizing bacterial biosynthetic genes for the phytotoxin coronatine, shown to have a role in plant pathogenesis."
	D'Eustachio	Multicellular animal	Human	Homo sapiens	PDF Abstract	How to get a GO molecular_function term more specific than GO:0004867 serine-type endopeptidase inhibitor activity to describe C1Inh protein?
	Drabkin	Multicellular animal	Mouse	Mus musculus	PDF Abstract	Several types of evidence codes are used in this paper; multiple markers can be annotated.
	Elsik	Multicellular animal	Honey bee	Apis mellifera	PDF Abstract	paper providing annotation for gene involved in neuromodulation
	Fey	Microorganism	Slime mold	Dictystelium discoideum	PDF Abstract	paper characterizing novel alpha kinase with one or two not so straight forward annotations.
	Fey	Microorganism	Slime mold	Dictystelium discoideum	PDF Abstract	"very typical, complex, Dictyostelium signal transduction paper"
	Gwinn	Bacteria (useful)	"Superbug, resistant to radiation"	Deinococcus radiodurans	PDF Abstract	This paper is a straightforward characterization of an enzyme's activity.
	Hance	Fungi	Yeast	Saccharomyces cerevisiae	PDF Abstract	Combining both GO and protein-protein interaction data in the prediction of protein function for unknown proteins.
	Heiges	Parasite	apicomplexan coccidian parasite	Cryptosporidum	PDF Abstract	This is a comparison of Cryptosporidium and Plasmodium. An example of the need for gene ontology comparisons among species of the same phylum where the cellular machinery and life-cycle stages significantly differ. The plasmodium community has been active in updating GO definitions to cover apicomplexans; are the definitions sufficient to cover cryptosporidium?
	Heiges	Parasite	apicomplexan coccidian parasite	Cryptosporidum	PDF Abstract	Cryptosporidium has acquired a large number of genes from distant phylogenetic sources (algal and eubacterial). An example of the need to make genome comparisons with unrelated species?
	Hood	Fungi		Neurospora crassa	PDF Abstract	This paper provides annotations for two genes that allow for efficient homologous recombination in Neurospora.
	Hood	Fungi		Neurospora crassa	PDF Abstract	This study identified a G(gamma) protein in Neurospora and characterizes its function and interaction with other G protein subunits.
	Howe	Multicellular animal	zebrafish	Danio rerio	PDF Abstract	"Authors report first characterization of the zebrafish robo4 gene and use antisense techniques to characterizes the role of this gene product in angiogenesis. This is a fairly straightforward paper, demonstrating IMP evidence with a clear choice of GO terms."
	Huntley	Plant	Mustard weed	Arabidopsis thaliana	PDF Abstract	"This paper describes characterization of an isoform of Arabidopsis Villin, several experiments demonstrate it's involvement in actin filament binding, organization and depolymerization."
	Joshi	Bacteria (symbiont: plant)	nitrogen-fixing symbiont of soybean	Bradyrhizobium japonicum	PDF Abstract	paper provides complete denitrification pathway of bacterium B.japonicum
	Joshi	Plant	Rice	Oryza sativa	PDF Abstract	paper mentions isolation and characterization of abiotic stress-inducible dehydrin gene in Rice
	Karalius	Plant	Tomato	Lycopersicon esculentum	PDF Abstract	Annotation for QTL involved in tomato brix
	Khodiyar	Multicellular animal	Human	Homo sapiens	PDF Abstract	"Cross species expts, how do we annotate these?"
	Louis	Insect vector		Anopheles gambiae	PDF Abstract	"A paper demonstrating a new role for annexin, again involving two organisms. Now what?"
	Louis	Multicellular animal	Mosquito	Anopheles gambiae	PDF Abstract	"A straightforward paper but known genes are assigned to several processes. Under which conditions GO terms become obsolete or new ones are added or old ones changed, etc? "
	Lu	Multicellular animal	"Mouse, rat"		PDF Abstract	A paper about function domain of rectifying K channels
	Lu	Multicellular animal	Mouse		PDF Abstract	A paper on cloning of a K-dependent Na/Ca exchanger protein
	Mao	Bacteria (symbiont: plant)	Rhizobia	Sinorhizobium meliloti	PDF Abstract	The paper used mutant analysis to annotate phbB and phbC genes involved in exopolysaccharide synthesis
	Master	Fungi		P. chrysosporium	PDF Abstract	A paper describing the secretome of a fungus grown on cellulose. Enzyme annotations described in this paper are commonly used in our Fungal Genome Project.
	Morris				PDF Abstract	EXTRACELLULAR (SECRETED PROTEINS APPEAR TO BE AN IMPORTANT PART OF THE REORTOIRE OF PLANT PATHOGENS.
	Morris				PDF Abstract	Avirulence genes(Avr) and the corresponding resistance genes(Rps) in their host form the basis of the interaction that results in race specific resistance of plants against pplant pathogens.
	Mueller	Plant	Tomato & pathogen	Solanum lycopersicum	PDF Abstract	A paper about interaction of pathogen proteins with tomato proteins. I'm not sure how such interactions between proteins from different organisms are annotated in GO.
	Mueller	Plant	Tomato	Solanum lycopersicum	PDF Abstract	Paper about a tomato fruit ripening gene rin.
	Pilcher	Microorganism	Slime mold	Dictystelium discoideum	PDF Abstract	paper invesigating kinesin family protein required for cytokinesis; several possible processes and components
	Purkayastha	Bacteria (pathogen: animal)	Q-fever pathogen	Coxiella burnetii	PDF Abstract	Experimental evidence suggests that acid phosphatase activity is a major virulence determinant in C. burnetii.
	Sakaniwa	Plant	Rice		PDF Abstract	Abnormal expression strategy.
	Sese	Fungi	Yeast	Saccharomyces cerevisiae	PDF Abstract	"introductory paper for morphological database and its data-mining functions on the web, which also contains some examples to reveal gene functions"
	Singh	Plant	Mustard weed	Arabidopsis thaliana	PDF Abstract	Identification of a gene responsible for enhanced pollen tube growth
	Singh	Plant	Rice		PDF Abstract	Gene involved in root cell shape
	Smith	Multicellular animal	Rat	Rattus	PDF Abstract	An older paper about cloning of rat alcohol dehydrogenases which raises a question about how granular the biological process term should be.
	Stover	Microorganism	Ciliate	Tetrahymena thermophila	PDF Abstract	"The authors present a number of hypotheses about the function of this distant Drosophila HP1 homolog, based on its cellular localization and sequence motifs. A typical paper in my field."
	Tanaka	Plant	Rice	Oryza sativa	PDF Abstract	rice chromosome1 paper from our Institute (Natl. Inst. Agrobiol. Sci.) (I would like to introduce the activity of our Institute)
	Tanaka	Plant	Mustard weed	Arabidopsis thaliana	PDF Abstract	"paper reporting the BZR1 gene functioning as a member of plant signaling pathway mediated by the plant hormones, Brassinosteroids (I would like to introduce an example of plant unique characteristics)"
	Topalis	Multicellular animal	Mosquito	Anopheles gambiae	PDF Abstract	"A straightforward paper describing many Odorant binding proteins in mosquitoes. All involved in olfaction, but is this the same biological process? Think of why some people are attractive to mossies and some not. "
	Tripathy	Pathogen (plant)	Oomycete	Phytophthora sojae	PDF Abstract	Avr1b-1 and Avr1b-2 are required for establishing infection in soybean and are closely located in the pathogen genome.
	Van Slyke	Multicellular animal	Zebrafish	Danio rerio	PDF Abstract	straitforward not too many genes.
	Yamasaki	Multicellular animal	Human	Homo sapiens	PDF Abstract	paper of annotation of human transcripts based on gene ontology
	Yamasaki	Multicellular animal	Human	Homo sapiens	PDF Abstract	GOAL: automated Gene Ontology analysis of expression profiles
	Yu	Multicellular animal	Human	Homo sapiens	PDF Abstract	This study utilized mRNA differential display and the Gene Ontology (GO) analysis to characterize the multiple interactions of a number of genes with gene expression profile involved in squamous cell cervical carcinoma.
	Yu	Multicellular animal	Frog	Xenopus laevis	PDF Abstract	applying multiple Support Vector Machines (SVM) for developing a large-scale annotation system.