SynRio - View Synechocystis 6803 chromosome using R and Shiny

Cretaed at:

National Facility for Marine Cyanobacteria

About SynRio


Welcome to Syn-R-io, an interactive R application based on the shiny package for visual exploration of Synechocystis 6803 chromosome with simple data extraction options

View Synechocystis genome as Circo or as a linear arrangement of genes. There are additional gene specific information retrival options and also some minimal data analysis features.


As a quick start, please refer the 'Help' section or click on the G-View tab and select 'Browser'

Quick start SynRio => (step 1) Click 'G-View' tab | (step 2) select 'Browser' option | (step 3) proceed to Data or Analysis tab

Legend

SynRio | Loading in progress...

Calculation in progress..

Calculation in progress..

SynRio | Loading in progress...

Navigator


Calculation in progress..




Download

Data download in progress..

Source: NFMC

Download

Locus Table is loading...

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Pathway table is loading...

Sequence Upstream in BP


          

          

Add annotation file


Select genes


Gene distance analysis is functional if genomic range is > 10000 bp

Please select Browser tab First...



                  

                  

                  




Please select Browser tab First...


subset data
Download

Introduction


Syn-R-io could be used for visualization of the Synechocystis genome as Circo or as linear gene viewer. There are additional gene specific information retrival options and also some minimal data analysis features.


G-View


Circos View

Synechocystis Genomic range with 50,000 BP size is viewable as Circos plot. Use the Dropdown menu to choose the range from S1-S72 and click the 'View' button




The circos plot gives a overview of genomic region highlighting plus and minus strands



The inner concentric circles represent COG and KEGG annotations with color codes as specified in the 'color codes' section(left side bar)


Browser View

1) View Gene locus using Synechocystis gene id

2) Choose 'Range Select' option to specify Genome region(From- To) or choose 'Genome segments' option (s1-s72) to view a 50,000bp range

3) Choose gene color based on COG or Kasuza annotation

4) Select Annotation tract and view the tracks in 9

5) Select check box to view zoom panel(10), navigation panel(11) toggle annotation track(8,9) and view user track

6) select genes from the dropdown, based on the gene browser view click the button to add the selected genes to gene cart

7) Genome plot

8) plot GC content

9) Annotation tracks, changes as per the selection in 4

10) Range selecter to zoom in to genome plot panel

11) Navigate to left and right of the genome locus

Data


Locus Datatable

1) Choose data type to download the options include, Gene, Promoter, Tatabox, Intergenomic region, Transcription unit, UTR, etc

2) Download data as .csv ot .txt

3) Data table


Extract Sequence

1) Select genome range to extract sequence

2) Specify genome range or upstream region in bp

3) Extracted sequence


Upload Geneset

1) Browse data file containing a list of gene ids

2) Specify data file structure

3) Choose header column from the uploaded file

4) Run to pick genes and add to gene cart

Analysis


Cluster Geneset

Important: Please select genome browser range before doing the cluster analysis!

1) Select Gene Distance option to pick gene set based on intergenic distance between genes

2) Specify Gene distance in BP

3) Data output based on gene distance number from 2

4) Choose a gene group

5) Add to gene cart

1) Choose Abiotic stress cluster to cluster gene set from genome browser range

2) Heatmap plot based on stress profile

1) Choose Go cluster to group genes based on Go terms

2) Distance plot output based on Go

3) Break as number of groups

Go groups based on Biological process

1) Choose to group genes based on KEGG pathway

2) Hirarchical plot based on KEGG pathways

3) Pathway group


Pattern Search

1) Choose between 'user pattern' or 'Pattern dataset' to select a genome pattern

2) Confirm or modify pattern

3) Select Exact if pattern is exact or deselect if the pattern has ambiguous letters. Check CPattern to include complement strand in the search

4) Search patteren in whole genome or only in upstream region

5) If upstream region is choosen pease select the number of base pairs

7) Density plot of the pattern

8) Download data


Network Views

1) Choose between 'Genesets' or 'user sets' to select a data source

2) Pick specific gene list

3) Choose protein network option to group genes based on PPI or KEGG categories to view KEGG based network or else select Go based associations

5) Choose network type

6) Color genes based onCOG or KEGG pathways

7) Gene networs plot

Color codes


KEGG Color


COG Color

Sample data


Highly expressed abiotic stress genes in Synechosystis genome