Genome Browser Manual

In the framework of well-defined gene structures, we integrated in-house generated monkey functional genomics data, as well as public available monkey data scattered in literatures and specialized databases, to develop a Genome Browser on the basis of ABrowse.

We re-analyzed the raw data and designed standardized criteria for meta-data extraction and storage. Tons of functional genomics data in rhesus macaque especially using the deep sequencing technology were integrated into the Genome Browser. Detailed meta-data such as sample information, types of experimental platforms and treatments, literature information, genotype-phenotype correlation information were carefully curated and integrated. Through the PubMed keywords query, we accessed all functional genomics studies in rhesus macaque, such as high-throughput annotations on gene expression profiles, transcription factor and microRNA binding sites generated by deep sequencing-based RNA-Seq, ChIP-Seq and CLIP-Seq technology. In addition, for each site in the monkey genome, we calculated cross-species conservation scores to facilitate rhesus macaque-centric comparative genomics studies.

More than 110 functional tracks were added onto the corresponding genomic context, illustrating refined gene and transcript structures, mRNA and EST data, RNA-Seq expression tags coverage and splicing junctions, transcription regulations, comparative genomics, variation and repeats, as well as phenotype and disease associations.

Generally Browse

The browser supports different searching methods for quick access to interesting tracks and provides a rapid and reliable display of any requested genomic region at multiple scales. Dozens of annotation tracks can be shown in the center panel according to specific user requirements.

Top Navigator

A navigation bar at the top of the browser allows users to search and configure tracks of interest quickly and easily.

Quick Search

"Quick Search" is the default tab on the search panel. To search for a track, enter search terms (chromosome location and species) into the box, then click "GO!"

Advanced Search

The "Advanced Search" allows users to search for browser by three manners:

1. Location Information: input the location information in the format of "chr:start-end" or "chr: start+length" for quick localization.
2. Fasta Format Sequences: Do alignment against monkey genome with sequence in FASTA format using BLAT. The result shows the highest identical hit(s) in sub-window. Users can also view the result on center panel by clicking "view". The result is recorded in "My Blat" on the "Righ-side Panel" (described below).
3. Keyword: Search track features like "id" with exact match and return hit(s) with hyperlink to corresponding genomic context.

Track Options

Dozens of annotation tracks are prepared in the Track Options (RhesusBase transcript structure, RefSeq genes, ESTs, mRNAs, CpG islands, etc.). The options correspond to the track clusters shown in the browser. Three display models are provided in normal view: general, dense and hide. The dense view shows the first entry of all entries presented in general view. Two display models are provided in basepair view: basepair and hide.

Create Landmark

If users are interested in one particular region or tracks, navigate to the region with the wanted tracks open then click "create landmark" to create landmark facilitating return this region next time. The landmark will be stored in "my landmark" on the right-side panel (described below). By clicking on the name of the landmark users created, users will be led to the corresponding region.

Chromosomal Ruler

The chromosomal ruler below the top navigator offers a quick and visualized locating in a specific region of the genome by clicking the corresponding location on it (compatible with FireFox, but not with IE).

Right-side Panel

Current Tracks

Show basic information of tracks displayed on the center panel.

Users can hide the tracks and change the order of tracks displayed on the screen by clicking the buttons shown as above. In order to move the tracks for convenient comparison, users need to drag the up-down button and move the information line to the desired place. Evaluations can be made to any tracks if signed in.

Entry Detail

Show detailed information of the designated region and a brief description about the track in which the region is located.

My Landmark

Record of searching results of "Create Landmark" on top navigator.

My Blat

Record of searching results of "Fasta Format Sequence" in advanced searching on top navigator.

My Tracks

Record of tracks users uploaded.

Main Window

Navigator Panel

At the top left corner of the center panel, navigation arrows are prepared for users to move the current screen in different directions. Zoom in or out of the current tracks by clicking "+" or "-". Users can use the magic wand in the middle of the navigation arrows to select one region of a track and zoom in in the main canvas or in a sub window. (Click the magic wand to active selecting status, then click a point on the center panel as the start point and release the mouse. Now click another point and the rectangle area between the two points is selected). A context menu will be showed for view and window choice.

View Panel

At the top right corner of the center panel, two buttons are provided for users to switch between "normal view" and "basepair view" conveniently.

Track Container

Show graphic information of tracks in browser.

User Registration and User Space

RhesusBase provides user space for customized data. By clicking the "Register Now" in the navigation bar, a registration page appears. After successful registration by filling in the required information, click on the "Sign In" to log in.

Add Comment for Entry

User can add comments for entries with private/public privilege. Public comments are visible among all users while private comments serve as personal online work notes.

Make Evaluation for Track

RhesusBase allows user to make track evaluation by adding stars and comments. One user can add comments many times but only once for star evaluation.

Upload & Manage My Tracks

User can freely upload data from web interface by setting the track name, genome name, file format, privilege and file path. Uploaded tracks will be listed in the "My Tracks" tab and the bottom of Current Track tab.

"Landmark" Record

Recording browsing status as a "landmark" allows for jumping to preserved important analysis status. RhesusBase also supports sharing landmark with specified users (Under construction).

Sequence Query Result Record

Sequence search results for guest are saved in the My Blat tab temporarily, but for registered user permanently.

Tracks

Mapping

CH SNP

This track shows SNPs mapped from CMSNP (Chinese Macaque within the Chinese Macaque SNP) database, which organizes rhesus macaque sequence variation data.

Phenotype and Disease Associations

GAD

This track shows the genomic positions of gene entries covered by GAD (Genetic Association Database), a gene-centered archive of human genetic association studies of complex diseases and disorders. liftOver was used to transform the GAD location from human to monkey.

Entry detail information was provided as follows:

Feature	Description
id	GAD ID
chr	Reference sequence chromosome
start	GAD region start position on genome
end	GAD region end position on genome
strand	+ or - for strand
length	=end-start

OMIM Genes

This track shows the genomic positions of all gene entries in the OMIM (Online Mendelian Inheritance in Man) database. The mappings displayed in this track are based on OMIM gene entries, their Entrez Gene IDs, and the corresponding RefSeq Gene locations.

GWAS

This track shows SNP-trait associations in GWAS (genome-wide association study) publications.

Genes and Gene Prediction

RhesusBase Genes

RNA-Seq data were analyzed with in-house pipelines and used to revise and assemble the monkey transcript structure. Powerful evaluations were carried out and the reasonable revised structure was confirmed.

Entry detail information is provided as follows:

Feature	Description
id	Transcript ID. For RhesusBase Genes, it's composed of "IMMRT1" and ten digitals. The first five ones refer to boundary refined, new exon, 5'UTR extended, 3'UTR extended and new transcript, respectively, when set to "1". The remaining five ones are the serial number associated with chromosome coordinate.
chr	Reference sequence chromosome or scaffold
start	Unsigned range Transcription start position
end	Unsigned range Transcription end position
strand	Strand of transcript (either '+' or '-')
length	=end-start
block_count	Number of blocks
block_start	Block start positions
block_end	Block end positions
block_size	Block sizes (equal to block-end-block_start)
block_frame	Block frame {0,1,2}, or -1 if no frame for exon
block_type	Five_prime_UTR/CDS/ three_prime_UTR
score	Range score
attribute	Additional information separated by semicolon. name2: Original Gene ID cdsStartStat: enum("none","unk","incmpl","cmpl") cdsEndStat: enum("none","unk","incmpl","cmpl") original transcript: original Ensembl transcript ID before revision cluster name: cluster ID where new transcript was clustered

Ensembl Genes

This track shows gene predictions generated by Ensembl. For a description of the methods used in Ensembl gene prediction, please refer to Hubbard, T. et al. (2002). Ensembl transcripts displayed are products of the Ensembl automatic pipeline, termed the Ensembl genebuild.

RefSeq Genes

This track shows known protein-coding and non-protein-coding genes taken from the NCBI RNA RefSeq (reference sequences) collection. The RefSeq collection is a freely accessible database of naturally occurring DNA, RNA, and protein sequences.

SGP Gene Predictions

This track shows gene predictions from the SGP program developed at the Genome Bionformatics Laboratory (GBL).

Geneid Gene Predictions

This track shows gene predictions from the geneid program developed at the Genome Bionformatics Laboratory (GBL). Please follow the hyperlink for more information about geneid.

NSCAN Gene Predictions

This track shows gene predictions using the N-SCAN gene structure prediction software provided by the Computational Genomics Lab at Washington University in St. Louis, MO, USA.

miRNA Genes

This track shows miRNA gene predictions based on the miRBase database.

tRNA

This track shows tRNA gene predictions made by the program tRNAscan-SE on complete or nearly complete genomes. Data come from Genomic tRNA Database.

mRNA and EST

mRNA

This track shows alignments between rhesus mRNAs in GenBank and the genome

Spliced EST

This track shows alignments between rhesus monkey expressed sequence tags (ESTs) in GenBank and the genome, showing signs of splicing when aligned to the genome.

Compared with EST track, a spliced EST must show evidence of at least one canonical intron, i.e. the genomic sequence between EST alignment blocks must be at least 32 bases in length and have GT/AG ends.

EST

This track shows alignments between rhesus monkey expressed sequence tags (ESTs) in GenBank and the genome, including spliced and non-spliced ESTs.

Other mRNA

This track displays alignment result (using Blat) of vertebrate and invertebrate mRNA in GenBank from organisms other than rhesus.

RhesusBase Junctions

This track shows alignments between the genome and junctions estimated by next-generation sequencing mapping tools with in-house RNA-Seq data.

Other Publication Junctions

This track shows alignments between the genome and junctions estimated by next-generation sequencing mapping tools with public RNA-Seq data, including Nature (2008,2011), Nature Biotechnology, Genome Research, PCB, JD and Yi).

RNA-Seq (IMM)

This track shows reads coverage of in-house RNA-Seq data mapping result of ten monkey tissues. In dense view, the higher score a region has, the higher reads coverage it indicates. The top limit of reads coverage is no more than one hundred reads, and the off-limit isn't shown on the screen.

Entry detail information was provided as follows:

Feature	Description
CHR	Reference sequence chromosome
START	Start position of a region with continuous identical coverage
LENGTH	Length of a region with continuous identical coverage
SCORE	Coverage of a region

RNA-Seq (Other)

Reads Coverage of RNA-Seq data from Nature, Nature Biotechnology, Genome Research, PCB, JD, Yi...

Regulation

TSS

This track shows transcription start sites in the rhesus genome, by methods described in " Ab initio identification of transcription start sites in the Rhesus macaque genome by histone modification and RNA-Seq. Nucl. Acids Res. (2010) doi: 10.1093/nar/gkq956."

CpG Island

This track shows regions of CpG islands, where CpGs are present at significantly higher levels than is typical for the genome as a whole. Following attributes were integrated:

Feature	Description
cpgNum	Number of CpGs in island
gcNum	Number of C and G in island
perCpg	Percentage of island that is CpG
perGc	Percentage of island that is C or G
obsExp	Ratio of observed(cpgNum) to expected(numC*numG/length) CpG in island

NHGRI BiPromoter

This track shows regions of NHGRI bidirectional promoters from NCBI. Bidirectional promoters are regulatory regions that fall between pairs of genes with an ability to regulate two downstream genes (divergent genes).

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.

miRNA Target

The 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 RefSeq RNA to monkey genome with a cut-off of 0.5 phastCons conservation score to gain miRNA target on monkey genes

Comparative Genomics

6way conservation

Conservation prediction score among 6 species including Human (hg18), Chimp (panTro2), Gorilla (gorGor3), Orangutan (ponAbe2), Rhesus (rheMac2) and Marmoset (calJac3) are provided. phastCons conservation score predicts region conservation and mostCons predicts most conserved elements from phastCons, while phyloP conservation score predicts basewise conservation. The predicting procedure starts with pairwise alignments between monkey and 5 species, respectively, data of which are downloaded from UCSC. Then the main tools including multiz, a multiple alignment tool, phastCons, a conservation predicting tool and phyloP, a basewise conservation predicting tool, were used successively to calculate the conservation prediction score.

9way conservation

The same with 6way, but three more species were involved to predict conservation, which were Mouse (mm8), Rat (rn4) and Opossum (monDom5).

Chain

This track shows alignments of monkey to other genomes using a gap scoring system that allows longer gaps than traditional affine gap scoring systems. The chain track displays boxes joined together by either single or double lines. The boxes represent aligning regions.

Net

The net track shows the best monkey/other chain for every part of the other genome. It is useful for finding orthologous regions and for studying genome rearrangement.

Variation and Repeats

dbSNP

This track shows short genetic variations, mostly single base variation, from NCBI dbSNP database.

RepeatMasker

This track shows interspersed repeats and low complexity DNA sequences using Arian Smit's RepeatMasker program. The program outputs a detailed annotation of the repeats that are present in the query sequence represented by this track. RepeatMasker uses the Repbase Update library of repeats from the Genetic Information Research Institute (GIRI).

This track displays up to ten different classes of repeats:

1. Short interspersed nuclear elements (SINE), which include ALUs
2. Long interspersed nuclear elements (LINE)
3. Long terminal repeat elements (LTR), which include retroposons
4. DNA repeat elements (DNA)
5. Simple repeats (micro-satellites)
6. Low complexity repeats
7. Satellite repeats
8. RNA repeats (including RNA, tRNA, rRNA, snRNA, scRNA, srpRNA)
9. Other repeats, which includes class RC (Rolling Circle)
10. Unknown

A "?" at the end of the "Family" or "Class" (for example, DNA?) signifies that the curator was unsure of the classification. At some point in the future, either the "?" will be removed or the classification will be changed.

Simple Repeats

This track displays simple tandem repeats (possibly imperfect repeats) located by TRF (Tandem Repeats Finder). These repeats can occur within coding regions of genes and may be quite polymorphic. Repeat expansions are sometimes associated with specific diseases.

CNV from DGV

This track displays copy number variations from DGV (Database of Genomic Variants).

CNV from dbVar

This track displays copy number variations from dbVar (Database of genomic structural variation ).

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