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Searches

Genview2 provides various tools with which to interrogate, view and annotate your gene expression data.

 

These tools are accessible upon dataset selection (see above), opening by default to the “Explore” gene/ transcript search query form.

Alternative means of data query are available via Gene Ontology and List tools (see below).

 

Search and View web form

 

The Explore query form allows your DEG analysis datasets to be queried by:

  1. Symbol – gene symbol/ transcript ID contained in your dataset.
  2. Synonym – NCBI RefSeq gene synonym/ transcript ID that map to genes in your dataset.
  3. Summary – a text string mapping to NCBI RefSeq summary text.
  4. View – previous search term else previously created list (see below)

Searches are case insensitive.

 

Search Example: Tyrosinase Related Protein 1

 

Gene symbol: TYRP1                   (column 5:  _DESeq2_transcriptDEG_results.txt file)

Transcript ID: NM_000550            (column 1:  _DESeq2_transcriptDEG_results.txt file)

Synonym: CAS2              (NCBI RefSeq gene_synonym entry for a gene in you results)

Summary: text string/ block         (NCBI RefSeq:

 

https://www.ncbi.nlm.nih.gov/nuccore/NM_000550

 

“Summary: This gene encodes a melanosomal enzyme that belongs to the tyrosinase family and plays an important role in the melanin biosynthetic pathway. Defects in this gene are the cause of rufous oculocutaneous albinism and oculocutaneous albinism type III.

[provided by RefSeq, Mar 2009].”

Valid search criteria

Assuming that your dataset contains an entry for Transcript NM_000550, valid search criteria would include any of the following:

 

 

Alternatively, previous search terms and previously created gene lists (see below) can be retrieved via the “View” drop down box.

 

 

 

Invalid Search Criteria

 

Data is only retrievable for genes/ transcripts that are present within your DEG dataset and it should be noted that searches by symbol and synonym are not interchangeable.

Search results

 

Search results will be displayed within the “IDs” list on an expanded “Explore” web page.

 

By default, a bar chart, analysis and annotation will be displayed for the first item in this list.

 

 

Where:

  1. The bar chart is generated from “DESeq2 normalized counts by sample”.
  2. Analysis results are derived from the DESeq2 transcript DEG results file.
  3. Annotation is retrieved from various external databases (see below).

 

Results for other transcripts in the list can be viewed by either directly clicking to select an ID, else by using “Previous” and “Next” buttons to scroll through the list, for example: NR_073131 (NEDD9)

 

 

 

Plots can be exported in PNG, JPEG, PDF or SVG format or printed directly.