t-Distributed Stochastic Neighbor Embedding (t-SNE): A tool for eco-physiological transcriptomic analysis
Advanced Search
Select up to three search categories and corresponding keywords using the fields to the right. Refer to the Help section for more detailed instructions.

Search our Collections & Repository

For very narrow results

When looking for a specific result

Best used for discovery & interchangable words

Recommended to be used in conjunction with other fields

Dates

to

Document Data
Library
People
Clear All
Clear All

For additional assistance using the Custom Query please check out our Help Page

i

t-Distributed Stochastic Neighbor Embedding (t-SNE): A tool for eco-physiological transcriptomic analysis

Filetype[PDF-5.58 MB]


Select the Download button to view the document
This document is over 5mb in size and cannot be previewed

Details:

  • Journal Title:
    Marine Genomics
  • Personal Author:
  • NOAA Program & Office:
  • Description:
    High-throughput RNA sequencing (RNA-Seq) has transformed the ecophysiological assessment of individual plankton species and communities. However, the technology generates complex data consisting of millions of short-read sequences that can be difficult to analyze and interpret. New bioinformatics workflows are needed to guide experimentation, environmental sampling, and to develop and test hypotheses. One complexity-reducing tool that has been used successfully in other fields is “t-distributed Stochastic Neighbor Embedding” (t-SNE). Its application to transcriptomic data from marine pelagic and benthic systems has yet to be explored. The present study demonstrates an application for evaluating RNA-Seq data using previously published, conventionally analyzed studies on the copepods Calanus finmarchicus and Neocalanus flemingeri. In one application, gene expression profiles were compared among different developmental stages. In another, they were compared among experimental conditions. In a third, they were compared among environmental samples from different locations. The profile categories identified by t-SNE were validated by reference to published results using differential gene expression and Gene Ontology (GO) analyses. The analyses demonstrate how individual samples can be evaluated for differences in global gene expression, as well as differences in expression related to specific biological processes, such as lipid metabolism and responses to stress. As RNA-Seq data from plankton species and communities become more common, t-SNE analysis should provide a powerful tool for determining trends and classifying samples into groups with similar transcriptional physiology, independent of collection site or time.
  • Keywords:
  • Source:
    Marine Genomics, 51, 100723
  • DOI:
  • ISSN:
    1874-7787
  • Format:
  • Publisher:
  • Document Type:
  • License:
  • Rights Information:
    CC BY
  • Compliance:
    Library
  • Main Document Checksum:
  • Download URL:
  • File Type:

Supporting Files

  • No Additional Files
More +

You May Also Like

Checkout today's featured content at repository.library.noaa.gov

Version 3.26.1