Gene Symbol RhesusBase Transcript ID Entrez ID Location Gene Type Gene Full Name RefSeq RNA/Protein Ensembl ID UniProt Accession InterPro Acc/Name/Signatures PubMed ID GO ID CAM ID

Gene Symbol	INSR
RhesusBase Transcript	IMMRT10011037116
Entrez ID	706009
Location	chr1:1-100000 / chr1:1+9999
Gene Type	protein-coding/tRNA
Gene Full Name	insulin receptor
RefSeq ID	NM_001032803/NP_001027975
Ensembl ID	ENSMMUG00000000001/ENSMMUT00000000001 /ENSMMUP00000000001
UniProt Accession	A0MJA5
InterPro Acc/Name/Signatures	IPR000001/Kringle/PR00545
PubMed ID	1301735
GO ID	0002001
CAM ID	CAM:0000123

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General Information

Assembly version

All annotations for rhesus macaque were compiled and presented on the basis of "Rhesus Jan. 2006 (MGSC Merged 1.0/rheMac2) assembly". "Human Mar. 2006 (NCBI36/hg18) assembly" and "July 2007 (NCBI37/mm9) assembly" were used to present human and mouse annotations, respectively.

Coordinate convention

Coordinates in RhesusBase are shown in the format of chromosome:start-end. All coordinates in RhesusBase are 0-based start except for additional notes.

Section title

For each gene, 8 categories of biological information were shown: Summary, Structure, Expression, Regulation, Variation, Phenotype and Disease, Function and Drug. Main category titles are highlighted in red, primary sub-titles in green and secondary sub-titles in blue.

Datasets

Overview

Dataset			Organism
			Monkey	Human	Mouse
Summary	IMM ID		RhesusBase Gene ID	N.A	N.A
	Entrez ID		NCBI Entrez Gene ID
	Human Entrez ID		N.A	Human Entrez Gene ID
	Offical Symbol		Gene Offical Symbol	N.A
	Location		Gene position
	Type		Gene type
	Full Name		Full gene name or description
	Lineage		Lineage of species
	RefSeq		RefSeq ID related to gene
	Ensembl		Gene Ensembl ID
	UniGene		Gene UniGene Cluster ID
	UniProt		Gene UniProt ID
	Publications		Publications about this gene
	Wiki		Wikipedia, WikiGenes and GeneCard information about this gene
	RefSeq Summary		Summary of this gene
Structure	Sequence	RNA	RNA sequences of this gene	N.A	N.A
		Protein	Protein sequences of this gene
Expression	BioGPS		N.A	A free extensible and customizable gene annotation portal, a complete resource for learning about gene and protein function.	N.A
	Allen Brain Microarray		N.A	Gene expression level analyzed from Allen Institute for Science Brain microarray analysis	N.A
	Allen Brain ISH		N.A	N.A	In situ hybridization data
Regulation	PTM		Post-translational modification from Experimental and HMM Prediction	N.A	N.A
	NATs	cisNATs	N.A	cis-Natural Antisense Transcripts from NATsDB
		transNATs	N.A	trans-Natural Antisense Transcripts from NATsDB
Variation	dbSNP		SNP information from NCBI dbSNP	SNP information from NCBI dbSNP and UCSC SNPs(130) track	N.A
	CNV	dbVar	Genomic structural variation from dbVar	N.A	N.A
		DGV	N.A	Genomic structural variation from Database of Genomic Variants	N.A
Phenotype and Disease	OMIM		N.A	Disease information from Online Mendelian Inheritance in Man	N.A
	GWAS		N.A	Genome-Wide Association Studies from NHGRI	N.A
	GAD		N.A	Genetic association studies of complex diseases and disorders from Genetic Association Database	N.A
	MGI	Marker	N.A	N.A	Marker from Mouse Genome Informatics
		Phenotypic Allele	N.A	N.A	Alleles and phenotypes from Mouse Genome Informatics
	piggyBac		N.A	N.A	information derived from PB insertions (Insert) in the mouse genome with piggyBac transposon system
Function	RIF		NCBI Gene References Into Functions which offers publications documenting experiments that add to the understanding of the gene and its function
	Pathway	KEGG	Pathway information from Kyoto Encyclopedia of Genes and Genomes	N.A	N.A
		PID	N.A	Biomolecular interactions and cellular processes from Pathway Interaction Database	N.A
		Reactome	N.A	Pathway information from Reactome	N.A
	InterPro		Predictive protein signatures used for the classification and automatic annotation of proteins and genomes from EBI InterPro	N.A	N.A
	Protein-Protein Interaction	STRING	Protein interacting with protein of this gene and scores of eight predicting methods from Search Tool for the Retrieval of Interacting Genes/Proteins	N.A	N.A
		HPRD	N.A	Protein interacting with protein of this gene, reference and other related information	N.A
		IntAct	N.A	Protein interacting with protein of this gene, publication, detection method and other related information	N.A
	Gene Ontology		N.A	Gene Ontology Term related to this gene, including Biological Process, Cellular Component and Molecular Function	N.A
Drug	PharmGKB	Overview	N.A	Overview information about this gene	N.A
		Related Gene		Genes related to this gene
		Related Pathway		Pathway this gene residents
		Related Drug		Drug related to this gene
		Related Disease		Disease related to this gene
	cMAP		N.A	Compound, Catalog Name and other information about the drug experiment on this gene	N.A

Dataset Introduction

Summary

Categories	Description
Entrez ID	NCBI Entrez Gene ID that is unique for certain gene
Offical Symbol	Nomenclature provided by the named external authority
Location	Chromosomal location of the gene, followed by the RefSeq chromosome and mRNA where the location comes from. The hyperlink to genome browser to view the genomic context was set
Type	Possible gene types in current RhesusBase release are protein-coding, pseudo, scRNA, snRNA, miscRNA, snoRNA and other. These are indexed as properties of a gene. More->>
Full Name	Full name of the gene, typically descriptions of the Offical Symbol
Lineage	Binomial and lineage from the Taxonomy database
RefSeq	Contains the RefSeq entries associated with the gene. Each group contains three RefSeq entries: the chromosome contig where the gene comes from, the RNA transcribed from the gene, the protein translated from the RNA. eg. : ( NW_001106399.1, XM_001094337.2, XP_001094337.2 ). More->>
Ensembl	Gene ID from Ensembl, a joint project between EMBL-EBI and the Wellcome Trust Sanger Institute to develop a software system which produces and maintains automatic annotation on selected eukaryotic genomes
UniGene	Cluster number from NCBI Unigene. Each UniGene entry is a set of transcript sequences that appear to come from the same transcription locus (gene or expressed pseudogene), together with information on protein similarities, gene expression, cDNA clone reagents, and genomic location
UniProt	Protein ID of UniProt, a database to provide the scientific community with a comprehensive, high-quality and freely accessible resource of protein sequence and functional information
Publications	Publication ID of PubMed, a literature database comprising more than 21 million citations for biomedical literature from MEDLINE, life science journals, and online books. It's citations may include links to full-text content from PubMed Central and publisher web sites
Wiki	The links to Wikipedia, WikiGenes and GeneCard. "Wikipedia is a multilingual, web-based, free-content encyclopedia project based on an openly editable model. The name "Wikipedia" is a portmanteau of the words wiki (a technology for creating collaborative websites, from the Hawaiian word wiki, meaning "quick") and encyclopedia. Wikipedia's articles provide links to guide the user to related pages with additional information." (Cite from "Wikipedia:About") "WikiGenes is the first wiki system to combine the collaborative and largely altruistic possibilities of wikis with explicit authorship. In view of the extraordinary success of Wikipedia there remains no doubt about the potential of collaborative publishing, yet its adoption in science has been limited. Here I discuss a dynamic collaborative knowledge base for the life sciences that provides authors with due credit and that can evolve via continual revision and traditional peer review into a rigorous scientific tool." (Cite from the article "A wiki for the life sciences where authorship matters") "GeneCards is a searchable, integrated, database of human genes that provides concise genomic related information, on all known and predicted human genes." (Cite from "GeneCard")

Structure

Sequence

RNA or protein sequences are presented in FASTA format. The sequence title, length and links to NCBI are shown. The coordinates flanking each sequence line indicates the positions of the first and last residues in the line.

Expression

Monkey

RNA-Seq

Several RNA-Seq datasets were analyzed and integrated, especially in-house strand-specific RNA-Seq data in ten rhesus macaque tissues. RhesusBase transcripts were used as the reference to estimate the expression levels in RPKM (Total reads mapped to exons of the transcript / (Total length in Kbp of exons of the transcript * Million Mapped reads)).

Human

RNA-Seq

RNA-Seq data were integrated from "Alternative isoform regulation in human tissue transcriptomes. Nature. 2008 Nov 27;456(7221):470-6.", "The evolution of gene expression levels in mammalian organs.Nature. 2011 Oct 19;478(7369):343-8." etc.. Raw RNA-Seq data in FASTQ format were re-analyzed and integrated with in-house pipelines. RefSeq transcripts were used as references to calculate gene RPKM.

BioGPS

Expression data was integrated from BioGPS, a free extensible and customizable gene annotation portal.

Column	Description
Sample	Tissue sample
log2 expression	Log2-transformed expression value
log2 expression level	Horizontal bar visualizing the log2-transformed expression value. Length of the bar of each sample was scaled so that the longest one fills up this column

User may select different probe-sets to browse or download expression information. Attention: in the download file, it's the original expression values rather the log2-transformed counterparts showed on page.

Allen Brain Microarray

Data integrated from Microarray of Allen Brain Atlas. For graphic interpretation, please refer to BioGPS section.

Column	Description
Structure	Name of brain regions, typically the top node for specific brain region on the "ontology tree of brain".
Ref. Structure	Representative sample for specific brain regions, selected on the basis of screening criteria as follows: The sample belongs to specific category of brain regions, based on the "ontology tree of brain" Samples with the highest gene expression were selected, with RIN number>7 For cases with low RNA quality (RIN number<7 in all samples), sample with the highest RIN number were selected
RIN	The RNA Integrity Number (RIN) is calculated on the basis of an algorithm for assigning integrity values to RNA quality. The RIN algorithm is applied to electrophoretic RNA measurements and based on a combination of different features that contribute information about the RNA integrity to provide a more robust universal measure.
Ref. Donor	Donor of "Ref.Structure"
log2 intensity	Log2-transformed RNA expression intensity of "Ref.Structure"
log2 intensity level	Log2-transformed RNA expression intensity represented in bar charts. Length of the bar is normalized by the highest expression intensity and visualized based on the expression intensity

Mouse

Brain ISH

Column	Description
Mouse Gene Symbol	Mouse gene symbol with hyperlinks to ISH gene pages in Allen Brain Atlas
Mouse Gene ID	Gene ID of mouse with hyperlinks to NCBI gene page
Mouse Gene Location	Mouse gene location in the format: <chromosome>:<start>-<end>
Expression Level ---------------------- Expression Density	Vertical bars in up-panel and down-panel visualize the expression levels and expression densities, respectively. Values ranged from 0 to 100. Each brain region was arranged horizontally. For more detail, refer to Allen Brain Atlas database

All data integrated from in situ hybridization data deposited in the Allen Brain Atlas database, a genome-wide, high-resolution atlas of gene expression throughout the adult mouse brain.

ISH data in 17 mouse brain regions were integrated:

• CB: Cerebellum
• CTX: Cerebral cortex
• HIP: Hippocampal region
• HPF: Hippocampal formation
• HY: Hypothalamus
• LSX: Lateral septal complex
• MB: Midbrain
• MY: Medulla
• OLF: Olfactory bulb
• P: Pons
• PAL: Pallidum
• RHP: Retrohippocampal region
• sAMY: Striatum-like amygdalar nuclei
• STR: Striatum
• STRd: Striatum dorsal region
• STRv: Striatum ventral region
• TH: Thalamus

Regulation

Monkey

PTM

Meta-data of this section were integrated from dbPTM, a database integrating experimentally verified Post-translational Modifications, as well as predicted PTMs on Swiss-Prot proteins.

Column	Description
UniProt Entry Name	The protein UniProt Entry Name with hyperlink to dbPTM Protein Information Page about this protein
Experimental	Quantity of Experimental Post-Translational Modification Sites. Please click [+] to expand details
HMM Prediction	Quantity of Predicted Post-Translational Modification Sites by profile HMM. Please click [+] to expand details

Detailed information after clicking [+]:

Column	Description
Location	Coordinate of the modified site on the protein
Modification and substrate	Modification type and its substrate. More>>
Resource	The original resource of the PTM
HMMER Bit Score	Bit Score and E-Value from HMMER. higher bit score and lower E-value indicate a more positive prediction
E-Value

TFBS

UCSC liftOver tool was used to transform Transcription Factor Binding Sites location from hg19 to rheMac2 supported by experimental ChIP-Seq data from ENCODE Project. TFBS overlapping upstream 10kbp of a gene were taken as its TFBS.

miRNA Target

miRNA target prediction software PicTar, miRanda and targetScan were used to predict miRNA target on human RefSeq RNA followed by AGO CLIP-Seq data filtering. UCSC LiftOver was used to transform human target sites to monkey genome with a minimal requirement of 0.5 phastCons conservation score.

Human

NATs

"NATs" (Natural Antisense Transcripts) are RNAs that are at least partially complementary to other endogenous RNAs. They might be transcribed in cis from opposing DNA strands at the same genomic locus (cisNATs) or in trans at separate loci (transNATs)."

We have integrated meta-data of cisNATs from NATsDB and transNATs from Trans-SAMap.

cisNATs

Column	Description
Cluster ID	NATsDB Cluster ID
Cluster Type	Cluster categories related to cis-NATs, named SA (Sense-Antisense pair) and NOB (Non-exon-Overlapping Bidirectional)
Plus Acc	Accession number of cis partner that can be aligned to plus strand
Plus Type	"Plus Acc" type, such as EST and mRNA
Plus Gene Symbol	Gene symbol on the locus plus partner
Plus Location	Location of plus partner
Overlap Length	Overlap length between two cis partners
Minus Acc	Accession number of cis partner that can be aligned to minus strand
Minus Type	"Minus Acc" type, such as EST, mRNA
Minus Gene Symbol	Gene symbol on the locus minus partner
Minus Location	Location of minus partner

transNATs

Column	Description
TU	Transcript Unit. Take the abbreviation of "hs_0_m.0" as an example "hs_" is the abbreviation of "human". The abbreviations for other species are shown below: Name of organisms (abbreviation/common name): hs (human) mm (mouse) The number 0 in "_0_" stands a cluster number. Trans-SAMap splits the chromosome into several clusters, each of which is not overlapped with one another and contains many transcript units Trans-SAMap endows every cluster with exclusive number "_m" stands for the strand orientation of the transcript. The "_m" (minus) means that this transcript is from minus strand; while "_p" is from plus strand The number 0 in ".0." means the first transcript unit in one strand of this cluster. Trans-SAMap also uses number to identify different transcript units
UniGene	UniGene cluster ID where the TU comes from
TU Ori	Orientation of TU
TU location	TU genome location
Alt.isoform	Alternative isoform ID of TU. These transcripts are predicted by SVAP. The last ".number", like ".118692", is a marker of transcript. ".118692" means one alternative isoform of transcript units other than the 118,692nd isoform of this transcript unit. This is a random number other than sorted number. Different transcripts from a gene have different IDs
AltIso Ori	Orientation of alternative isoform
AltIso location	Location on genome of alternative isoform
Target isoform	Like alternative isoform, but target isoform rather alternative isoform
Target Iso Ori	Orientation of target isoform
Target location	Location on genome of target isoform

Mouse

NATs

Refer to Human NATs

Variation

Monkey

dbSNP

All meta-data was integrated from NCBI dbSNP.

Column	Description
RefSNP ID	SNP reference ID
Location	SNP Genomic location
Alleles	SNP Alleles
IUPAC	Alleles defined by the International Union of Pure and Applied Chemistry (IUPAC). It could be: IUPAC code Description A A C C G G T T M A or C R A or G W A or T S C or G Y C or T K G or T V A or C or G H A or C or T D A or G or T B C or G or T N G or A or T or C
Variation Class	SNP Variation class including "Strict SNP", "Insertion/deletion variation", "Unclassified heterozygous variations", "Microsatellite", "Named variation without allele sequence", "No variation", "Mixed variations" or "Multinucleotide polymorphism"
Molecule Type	Type of the molecule from which this SNP is validated
UpStream	Click the [+] to display upstream sequence of this SNP
DownStream	Click the [+] to display downstream sequence of this SNP

CNV

CNVs (Copy-number variations)--a form of structural variation--are alterations of the DNA of a genome that results in the cell having an abnormal number of copies of one or more sections of the DNA. CNVs correspond to relatively large regions of the genome that have been deleted (fewer than the normal number) or duplicated (more than the normal number) on certain chromosomes. For example, the chromosome that normally has sections in order as A-B-C-D might instead have sections A-B-C-C-D (a duplication of "C") or A-B-D (a deletion of "C"). (cite Wikipedia "Copy-number variation")

dbVar

dbVar is a NCBI database of genomic structural variation.

All meta-data were integrated from nstd3 study in the publication of Lee et al. 2008. If the location of structural variant overlaps with the gene location, the structural variant was considered as the structural variant of the gene.

Column	Description
Variant Acc	dbVar Variant accession ID
Location (0-based)	Variant genomic location
Method Type	Variant detection method
Validation	Whether the variant was validated
Allele Type	Allele type of variant call

Human

dbSNP

All meta-data were integrated from NCBI dbSNP and UCSC SNPs130 track.

Column	Description
RefSNP ID	dbSNP Reference SNP ID
Location (1-based)	SNP genomic location
Strand	DNA strand where alleles observed
refNCBI	Reference genomic sequence from dbSNP
refUCSC	Reference genomic sequence from UCSC lookup of chrom, chromStart, chromEnd
Alleles	The sequences of the observed alleles from rs-fasta files
Molecule Type	Sample type from exemplar submitted sequence (ss)
Class	Class of variant (single, in-del, named, mixed, etc.)
Valid	Validation status of the SNP
Function	Functional category of the SNP (coding-synon, coding-nonsynon, intron, etc. Only SNPs with function of coding-synon, nonsense, missense and frameshift were collected in RhesusBase!)
LocType	Type of mapping inferred from size on reference; may not agree with class

CNV

DGV

DGV (Database of Genomic Variants) is a database that provides a comprehensive summary of structural variation in the human genome. It defines structural variation as genomic alterations that involve segments of DNA that are larger than 50bp. DGV only represents structural variations identified in healthy control samples..

Column	Description
Variation ID	Variation ID assigned to every record in the DGV
Landmark (1-based)	Physical position of a record based on coordinates, clones, genes, or other features for which a physical position can be established. All coordinates are currently based on May 2004 (NCBI Build35) Assembly of the Human Genome
Human location (1-based)	Genomic location where the variant located
PubMed	PubMed ID for the study from which the information is extracted
Method/Platform	The method by which the variation is discovered/characterized
Frequency	Allele Frequency

Mouse

There is no available variation information about Mouse in the current release of RhesusBase.

Phenotype and Disease

Monkey

There is no available phenotype and disease information about Monkey in the current release of RhesusBase.

Human

OMIM

"OMIM (Online Mendelian Inheritance in Man) is a comprehensive, authoritative, and timely compendium of human genes and genetic phenotypes. The full-text, referenced overviews in OMIM contain information on all known mendelian disorders and over 12,000 genes. OMIM focuses on the relationship between phenotype and genotype. " (cite NCIB OMIM)

Column	Description
OMIM Number	OMIM ID
Location	OMIM gene location on monkey genome transformed from human by liftOver
Human Location	OMIM gene location on huan genome
Chr Band	Human chromosome band
Title	OMIM gene title
Disorder	Disorder associated with the OMIM gene
Method	The method for mapping genes. More>>

GWAS

"GWAS (The genome-wide association study) publications listed here include only those attempting to assay at least 100,000 single nucleotide polymorphisms (SNPs) in the initial stage. Publications are organized from most to least recent date of publication, indexing from online publication if available. Studies focusing only on candidate genes are excluded from this catalog." (cite NHGRI GWAS Catalog)

Column	Description
Reported Genes	Reported Genes
Mapped Genes	Mapped Genes
Date Added to Catalog	Date Added to Catalog
First Author/ Date/ Journal/ Study	First author/Date/Journal of publication and PubMed ID of publication of the study
Initial Sample Size	Initial sample size
Replication Sample Size	Replication sample size
Risk Allele	Strongest SNP-Risk Allele
Risk Allele Freq	Risk Allele Frequency
SNPs	ID of SNP associated with trait
Context	Context of the SNP
P-value	P-Value
OR or beta-coefficient and [95% CI]	Odds ratio or beta and 95% Confidence Interval
Disease/Trait	Disease or trait assessed in study
Region/ Location	Chromosome band / location of SNP
Platform [SNPs passing QC]	Platform and [SNPs passing QC]

GAD

GAD (The Genetic Association Database) is an archive of human genetic association studies of complex diseases and disorders. This includes summary data extracted from published papers in peer reviewed journals on candidate gene and GWAS studies. (cite GAD)

Column	Description
GAD ID	GAD ID
Disease Class	Disease Class
OMIM ID	OMIM ID associating with this disease
Human Gene ID	Human Entrez Gene ID associated with this disease
PubMed	PubMed ID associated with this disease
rs Number	dbSNP ID

Mouse

MGI

MGI (Mouse Genome Informatics) is the international database resource for the laboratory mouse, providing integrated genetic, genomic and biological data to facilitate the study of human health and disease.

Marker

Marker provides basic detail of gene and associated diseases with mutation alleles related to corresponding gene.

Phenotypic Allele

The Phenotypic allele project enables access to spontaneous, induced, and genetically-engineered mutations and their strain-specific phenotypes. Phenotypic alleles related to the gene were integrated with hyperlink to MGI website.

piggyBac

All meta-data were integrated from PBmice.

The TTAA-specific transposon piggyBac is rapidly becoming a highly useful transposon for genetic engineering of a wide variety of species, particularly insects. piggyBac provides information related to piggyBac in particular, and its uses for transgenesis in general. (cite piggyBac)

Column	Description
Symbol	Gene Symbol
Insert Name	Name of insertion sequence
Strain	Strain
Chr	Chromosome Number
Pos	Position
Line Name	Line Name

Function

Monkey

RIF

GeneRIF (Gene Reference Into Function) provides a simple mechanism for scientists to add to the functional annotation of Entrez Gene. It is intended to facilitate access to publications documenting experiments that add to the understanding of a gene and its function. References related to the function of gene in Monkey were provided.

Pathway

KEGG

KEGG (Kyoto Encyclopedia of Genes and Genomes) is a bioinformatics resource for linking genomes to life and the environment, providing a collection of online databases dealing with genomes, enzymatic pathways, and biological chemicals. Map, pathway, compound, drug and glycan information related to the gene were provided.

InterPro

InterPro is a database of protein families, domains and functional sites in which identifiable features found in known proteins can be applied to new protein sequences in order to functionally characterise them. The information related to the gene was provided as follows: Domain predicted by IntreProScan, Signatures to other domain database, GO terms assigned to the domain and PDB entries of the domain.

Protein-Protein Interaction

STRING

STRING (Search Tool for the Retrieval of Interacting Genes/Proteins) is a database of known and predicted protein interactions. The interactions include direct (physical) and indirect (functional) associations; they are derived from four sources: Genomic Context, High-throughput Experiments, (Conserved) Coexpression, Previous Knowledge..

Column	Description
Protein2	Ensembl protein ID interacting with protein of the gene
Gene2	Symbol of gene encoding "Protein2"
Neighborhood	Neighborhood score computed from the inter-gene nucleotide count
Gene Fusion	Gene Fusion score derived from fused proteins in other species
Concurrence	Concurrence score of the phyletic profile derived from similar absence/presence patterns of genes
Coexpression	Coexpression score derived from similar pattern of mRNA expression measured by DNA arrays and similar technologies
Experimental	Experimental score derived from experimental data, such as, affinity chromatography
Database	Database score derived from curated data of various databases
Textmining	Textmining score derived from the co-occurrence of gene/protein names in abstracts
Combined score	Combined score computed by combining the probabilities from the different evidence channels, correcting for the probability of randomly observing an interaction

All above scores were scaled into 0-1000.

Human

RIF

The section shows total references related to the function of the gene in Human. For more details about RIF, please refer to RIF in Monkey.

Gene Ontology

The Gene Ontology project is a major bioinformatics aiming at standardizing the representation of gene and gene product attributes across species and databases. The project provides a controlled vocabulary of terms for describing gene product characteristics, its annotation data from GO Consortium members, as well as tools to access and process this data.

The cellular component ontology describes locations, at the levels of subcellular structures and macromolecular complexes. Examples of cellular components include nuclear inner membrane, with the synonym inner envelope, and the ubiquitin ligase complex, with several subtypes of these complexes represented.

The molecular functions of a gene product are the jobs that it does or the "abilities" that it has. These may include transporting things around, binding to things, holding things together and changing one thing into another. This is different from the biological processes the gene product is involved in, which involve more than one activity.

A biological process is a recognized series of events or molecular functions. A process is a collection of molecular events with a defined beginning and end. Mutant phenotypes often reflect disruptions in biological processes. (Cite GO)

Column	Description
GO ID	Gene Ontology ID
GO term	Terms for describing gene product characteristics and annotation data from GO Consortium
Ontology	Biological Process/Cellular Component/Molecular Function
Evidence	Evidence supporting the annotations
Reference	Reference associating to certain GO ID

Pathway

PID

PID (The Pathway Interaction Database) is a highly-structured, curated collection of information about known biomolecular interactions and key cellular processes assembled into signaling pathways. ID and name of pathways in which the corresponding gene involved were provided.

Reactome

REACTOME is an open-source, open access, manually curated and peer-reviewed pathway database. Names of associated pathway of gene are provided.

Protein-Protein Interaction

HPRD

HPRD (The Human Protein Reference Database) represents a centralized platform to visually depict and integrate information pertaining to domain architecture, post-translational modifications, interaction networks and disease association for each protein in the human proteome. Information of interactor with gene are provided, such as interactor symbol, interactor name, experiment type and so forth.

IntAct

IntAct provides a freely available, open source database system and analysis tools for protein interaction data.

Mouse

RIF

There is no available function information about Mouse in the current release of RhesusBase.

Drug

Monkey

There is no available drug information about Monkey in the current release of RhesusBase.

Human

PharmGKB

PharmGKB (Pharmacogenomics Knowledge Implementation.) is a comprehensive resource that curates knowledge about the impact of genetic variation on drug response for researchers and clinicians. Encompass clinical information were encompassed, including dosing guidelines and drug labels, potentially clinically actionable gene-drug associations and genotype-phenotype relationships (cite PharmGKB). Information related to the gene was provided as follows: overview information, gene related to the corresponding gene, pathway in which corresponding gene is involved, related drug and related disease.

cMAP

cMAP (Connectivity Map) is a collection of genome-wide transcriptional expression data from cultured human cells treated with bioactive small molecules and simple pattern-matching algorithms that together enable the discovery of functional connections between drugs, genes and diseases through the transitory feature of common gene-expression changes. Basic information of related small molecules from ChemBank in cMAP was provided. The compound were classified into two categories by expression fold change (FC). FC >=2 is considered as up-regulation compound and <=0.5 as down-regulation one.

Mouse

There is no available drug information about Mouse in the current release of RhesusBase.