PATRIC November 2012 Release Introduces New Transcriptomics Data and Analysis Tools and over 370 New Genomes

Published on 2012-12-10

Transcriptomics Capabilities

We are pleased to announce the availability of curated transcriptomics data and related data analysis and visualization tools on the PATRIC website.  In addition to integration of a large number of published gene expression datasets related to bacterial pathogens from NCBI’s GEO database (http://www.ncbi.nlm.nih.gov/geo/), we provide a suite of integrated tools that allow you to explore, visualize, analyze, and compare published gene expression datasets available at PATRIC.  You may now also privately and securely upload and analyze your own unpublished gene expression data, generated by microarray or RNA-Seq technologies, and compare it with other published datasets.

New Transcriptomics functionality includes:

  • View lists of transcriptomics datasets available at PATRIC.  Filter the list of Experiments or Comparisons based on manually curated metadata (such as Organism, Strain, Gene Modification, and Experimental Condition) to quickly find experiments of interest.
  • Select one or more experiments and generate a dynamic Gene List.  You can filter the gene list based on Log Ratio or Z-score cut-off, up/down regulation, or gene functions.  You can also save your selection(s) as a group in your Workspace for future use.
  • Analyze the data using the Heatmap Viewer and clustering to quickly find genes that are similarly expressed across one or more comparisons.
  • Select a subset of genes and view corresponding metabolic pathways.
  • For a gene of interest, view all available transcriptomics data.  Use keyword search to see the expression of the gene under selected experimental conditions.  Apply Log Ratio or Z-score cut-off to find top experimental conditions or genetic modifications causing differential expression of the gene, which may help to assign potential function to a hypothetical gene.
  • For a gene of interest, see all the genes that are positively or negatively correlated based on gene expression ratio.  This may help to identify genes that are co-regulated or have similar functions.
  • Upload your own transcriptomics data, generated by microarray or RNA-seq technologies to your private workspace and analyze it using annotations and analysis tools available at PATRIC.  You can also compare your data with other transcriptomics datasets within PATRIC.

A summary of the number of transcriptomics datasets currently available at PATRIC:

Organism

Experiments

Comparisons

Escherichia

215

1284

Mycobacterium

45

549

Salmonella

39

313

Streptococcus

75

297

Streptomyces

7

224

Clostridium

9

151

Staphylococcus

22

138

Listeria

31

106

Helicobacter

7

88

Saccharopolyspora

2

50

Yersinia

6

46

Lactococcus

7

22

Brucella

5

11

Lactobacillus

1

3

Shigella

1

3

Shewanella

2

2

Fore more information on transcriptomics data, related analysis tools and how to use them, please visit Transcriptomics Data FAQs.

Genomes and Annotations

In the November 2012 data release, 387 new genomes have been added and 370 of them have been annotated using RAST. Sixteen genomes have been updated or replaced with the newer versions.

A summary of the genomes available on the PATRIC website through November 2012 is provided in the table below.

PATRIC

RefSeq

Number of genomes

7012

6089

Number of Complete genomes

1981

1968

Number of WGS genomes

5029

3722

Number of Plasmid only genomes

2

399

** **