mingchen0919 / pag-2017-computer-demo

PAG 2017 computer demo

• HGD Database Navigation
• Tripal Elasticsearch
• Tripal Expression Analysis

HGD Database Navigation

Genetic resources

• transcriptomes from 15 species (click Genomic Data->Transcriptomes->Fraxinus pennsylvanica 120313)

  • transcriptome analysis information
  • assembly reports
  • annotation data downloadable
  • raw reads links to NCBI SRA

• SSRs (click Genomic Data->gSSRs)

  • predicted transcriptomic SSRs (15 species)
  • predicted genomic SSRs (10 species)
  • confirmed SSRs markers (8 species)

• Reference genome

  • Chinese Chestnut Genome and QTL Sequences v1.0 (click Genomic Data->Chestnut Genome)
  • Chestnut Physical Map (click Genomic Data->Chestnut Physical Map)

• Organism page (Click Trees->Fraxinus pennsylvanica: http://www.hardwoodgenomics.org/organism/Fraxinus/pennsylvanica)

  • Brief introduction to a species
  • Links to all genetic resources that are associated with this species.

Tools

• Cmap (Tools->Cmap)
• JBrowse/Webapollo (Tools->JBrowse/WebApollo - Chestnut Genome Sequence)
• SyMap (Tools->Chinese Chestnut SyMAP)
• Blast
• Expression Visualization

Tripal Elasticsearch

Site wide search (Advanced search)

• Wildcard search with *. Examples:

  • genom* sequence -> genome, genomic, genomics ...
  • Lir*dron tulipifera -> Liriodendron tulipifera

• Fuzzy search: When you don't know how to exactly spell your keywords, you use fuzzy search. fuzzy search allows you to search for similar words. You use the ~ at the end of your keyword for fuzzy search (keyword~). Examples:

  • sequeeence~ -> sequence
  • Alnus rhmifolia~ -> Alnus rhombifolia

• Regular expression search: wrapping keywords with forward slash (/). Examples:

  • /transcriptom[a-z]+/ -> transcriptome, transcriptomes, transcriptomics ...

• Boolean operators: + and -. + means must present; - means must not present. Examples:

  • +"green ash" +transcriptome -genome
  • +"green ash" -transcriptome +genome

• AND, OR, NOT operator and combination search. Examples:

  • "heat stress" AND ("Castanea mollissima" OR "green ash") NOT "heat shock"

Database table specific search

The Tripal Elasticsearch module allows you to index single tables and build search interface for them. All the advanced search methods that are available to the site wide search can be applied to table specific search.

Implementation examples in the HGD

• transcripts search (A couple of examples):

  1. search keywords:
  • Abbreviation: Fraxinus pennsylvanica
  • Unique name:
  • Hit Description: "heat shock"
  2. search keywords:
  • Abbreviation: Fraxinus pennsylvanica
  • Unique name:
  • Hit Description: "heat shock" NOT "Arabidopsis thaliana"

• Organisms

• Search with no keywords input will return all available records

• Search results downloadable as csv file.

• Search interfaces and results are displayed with separated drupal blocks.

Tripal Expression Analysis

Data collection

• Example: http://www.hardwoodgenomics.org/feature/Fraxinus_pennsylvanica_120313_comp61194_c0_seq5

  • Expression data analysis information: click Analyses->Green Ash Ozone Treatments to go to the analysis content page
  • Biomaterials information: click Expression->Any bar of the figure to go to the biomaterial content page
  • Expression values: see the figure(sort, tile/chart).

Genes Expression Visualization

• Go to the Expression Visualization interface
• Provide a list of genes separated by comma(,)
• Click Display Expression Heatmap button to generate the heatmap.
• Some example genes:

Fraxinus_pennsylvanica_120313_comp18083_c0_seq1,
Fraxinus_pennsylvanica_120313_comp15550_c0_seq1,
Fraxinus_pennsylvanica_120313_comp13944_c0_seq1,
Fraxinus_pennsylvanica_120313_comp64929_c0_seq2,
Fraxinus_pennsylvanica_120313_comp52334_c0_seq1,
Fraxinus_pennsylvanica_120313_comp56548_c0_seq1,
Fraxinus_pennsylvanica_120313_comp56481_c0_seq1,
Fraxinus_pennsylvanica_120313_comp56481_c0_seq2,
Fraxinus_pennsylvanica_120313_comp56481_c0_seq3,
Fraxinus_pennsylvanica_120313_comp56092_c0_seq1

A use case: expression comparison between heat shock vs kinase genes from green ash.

Heat shock induced gene expression can help limit the damage caused by stress(Arya, et al., 2007).

• Go to transcripts search interface (click Transcripts search)

  • Search "heat shock" for Hit Description and select Fraxinus pennsylvanica for Abbreviation, and download the search results.
  • Search kinase NOT heat for Hit Description and select Fraxinus pennsylvanica for Abbreviation, and download the search results.

• Search keywords: "heat shock" genes(heat-shock-genes.txt)

Fraxinus_pennsylvanica_120313_comp59663_c0_seq1,
Fraxinus_pennsylvanica_120313_comp59663_c0_seq2,
Fraxinus_pennsylvanica_120313_comp56723_c0_seq1,
Fraxinus_pennsylvanica_120313_comp60325_c0_seq16,
Fraxinus_pennsylvanica_120313_comp61194_c0_seq4,
Fraxinus_pennsylvanica_120313_comp61194_c0_seq5,
Fraxinus_pennsylvanica_120313_comp61194_c0_seq8,
Fraxinus_pennsylvanica_120313_comp61194_c0_seq6,

• Search keywords: +kinase -heat genes(kinase-not-heat-genes.txt)

Fraxinus_pennsylvanica_120313_comp59251_c0_seq8,
Fraxinus_pennsylvanica_120313_comp31358_c0_seq1,
Fraxinus_pennsylvanica_120313_comp63273_c0_seq25,
Fraxinus_pennsylvanica_120313_comp63273_c0_seq3,
Fraxinus_pennsylvanica_120313_comp48376_c0_seq1,
Fraxinus_pennsylvanica_120313_comp48376_c0_seq2,
Fraxinus_pennsylvanica_120313_comp40803_c0_seq1,
Fraxinus_pennsylvanica_120313_comp31272_c0_seq1

• Go to Expression Visualization interface to generate the heatmap.