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    <label class="control-label" id="select.genome-label" for="select.genome-selectized">Genome</label>
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                  Expression table
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Text Content

Upland Cottons Pangenome
 * Home
 * Gene expression
 * Genomic variations
 * Genic space
 * Help
 * Contact








STRUCTURAL VARIATION AND GENE EXPRESSION ACROSS UPLAND COTTON CULTIVARS


Genetic mapping serves as an important tool for biologists to determine the
genetic architecture of large-effect variants on traits of interest. However,
the translation of these findings into practical applications for breeders has
historically been fragmented. Bridging this gap involves the identification of
assayable markers for marker-assisted selection and the pinpointing of candidate
genes for modification. With the advent of multiple reference genomes, rich
diversity data, and high-confidence gene annotations, all of the raw materials
are available for identifying high-value molecular targets for breeding.
However, a computational framework to make use of these data does not exist yet
for cotton. To address this gap, we are developing an extensible and accessible
framework to leverage our multiple high-quality reference genomes of the complex
and polyploid cotton crop to effectively find targets for molecular breeding
efforts.

This website provides a hub for access to the upland cotton pangenome resource,
subject to the data usage policy.


CITING UPLAND COTTONS PANGENOME

Sreedasyam,A., Lovell, J.T., Jones, D.W., Schmutz, J., et al. Pan-genome
integration of genetic diversity to accelerate molecular breeding in cotton.
Unpublished.


CONTACTS



 * Avinash Sreedasyam (asreedasyam AT hudsonalpha DOT org)
 * John Lovell (jlovell AT hudsonalpha DOT org)
 * Don Jones (DJones AT cottoninc DOT com)
 * Jeremy Schmutz (jschmutz AT hudsonalpha DOT org)




--------------------------------------------------------------------------------

The Upland Cottons Pangenome project conducted by the HudsonAlpha Institute for
Biotechnology was supported by the USDA-NIFA-AFRI grant (1028379) and genome
annotation was supported by the U.S. Department of Energy Joint Genome Institute
(JGI), funded by the Office of Science of the U.S. Department of Energy (DOE).
HudsonAlpha Institute for Biotechnology, Genome Sequencing Center | 601 Genome
Way NW, Building 601, Huntsville, AL 35806
Genome
Gossypium hirsutum var. TM1 v3.2
Gossypium hirsutum var. TM1 v3.2

Expression unit
FPKM
FPKM


--------------------------------------------------------------------------------

Expression table


 * Data
 * Visualization
 * Orthologs

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nTop variable genes
Variable genes heatmap

--------------------------------------------------------------------------------

Genes of interest heatmap
Submit






Heatmap data
Loading...



Orthologs genome

Genes of interest (GOI)
Single copy orthologs
Submit Use examples

Orthologs table

Orthologs expression

GOI expression






Loading...



Loading...





--------------------------------------------------------------------------------

The Upland Cottons Pangenome project conducted by the HudsonAlpha Institute for
Biotechnology was supported by the USDA-NIFA-AFRI grant (1028379) and genome
annotation was supported by the U.S. Department of Energy Joint Genome Institute
(JGI), funded by the Office of Science of the U.S. Department of Energy (DOE).
HudsonAlpha Institute for Biotechnology, Genome Sequencing Center | 601 Genome
Way NW, Building 601, Huntsville, AL 35806






Reference
Query
Genome
TM1
TM1

Chromosome
A01
A01

Start
End
bp Mbp
Submit
Clear


Loading...





--------------------------------------------------------------------------------

The Upland Cottons Pangenome project conducted by the HudsonAlpha Institute for
Biotechnology was supported by the USDA-NIFA-AFRI grant (1028379) and genome
annotation was supported by the U.S. Department of Energy Joint Genome Institute
(JGI), funded by the Office of Science of the U.S. Department of Energy (DOE).
HudsonAlpha Institute for Biotechnology, Genome Sequencing Center | 601 Genome
Way NW, Building 601, Huntsville, AL 35806






Reference genome
Ghirsutum
Ghirsutum

Loading...





--------------------------------------------------------------------------------

The Upland Cottons Pangenome project conducted by the HudsonAlpha Institute for
Biotechnology was supported by the USDA-NIFA-AFRI grant (1028379) and genome
annotation was supported by the U.S. Department of Energy Joint Genome Institute
(JGI), funded by the Office of Science of the U.S. Department of Energy (DOE).
HudsonAlpha Institute for Biotechnology, Genome Sequencing Center | 601 Genome
Way NW, Building 601, Huntsville, AL 35806





UPLAND COTTONS PANGENOME - HELP


 * GENE EXPRESSION

   
      
   
    * DATA
   
      Under data tab gene expression levels for a selected species are tabulated
      in the main panel. By default, expression levels (FPKM) are displayed for
      Arabidopsis across all available experiments.
   
      FILTER AND SEARCH GENES
   
      You can select species and experiments available in the project and narrow
      down the results using drop down menus in the left panel. Also, you can
      select FPKM or TPM expression levels.
   
      The tabular data in the main panel is interactive allowing one to re-order
      the data using sorting arrows by the column names. You can filter the
      content using the Search box on the right. This search works not only with
      Gene IDs but also with the gene function descriptions. Furthermore,
      selecting a gene ID or a row in the table displays the gene information
      (including location and function description) in the top panel.
   
      
      
      
      
   
      DOWNLOADS
   
      Expression data, sample information and function descriptions can be
      directly downloaded as CSV files by clicking Download buttons in the left
      panel.
   
      
      
   
    * VISUALIZE EXPRESSION PATTERNS
   
      In visualization tab, you can generate a heatmap displaying top variable
      genes (default, 20) across selected experimental conditions. For a list of
      your genes of interest, you can see the variation in their expression
      across available samples in a particular experiment.
   
      
      
   
    * EXPRESSION PROFILES OF ORTHOLOGOUS GENES
   
      In orthologs tab you can find the expression pattern of ortholog/s of a
      single or multipe genes from a selected species. Here you can visualize
      expression profiles of both, orthologs from selected species (top) and the
      queried species (bottom).
   
      You can filter for only single copy orthologs using the check box.
   
      Orthologous genes, expression of orthologs and expression of your genes of
      interest can be downloaded as CSV files by using download buttons at the
      bottom.




--------------------------------------------------------------------------------

The Upland Cottons Pangenome project conducted by the HudsonAlpha Institute for
Biotechnology was supported by the USDA-NIFA-AFRI grant (1028379) and genome
annotation was supported by the U.S. Department of Energy Joint Genome Institute
(JGI), funded by the Office of Science of the U.S. Department of Energy (DOE).
HudsonAlpha Institute for Biotechnology, Genome Sequencing Center | 601 Genome
Way NW, Building 601, Huntsville, AL 35806






GENE EXPRESSION

DATA VISUALIZATION ORTHOLOGS

GENOMIC VARIATIONS

GENIC SPACE






CONTACT


 * AVINASH SREEDASYAM (ASREEDASYAM AT HUDSONALPHA DOT ORG)
   
   
 * JOHN LOVELL (JLOVELL AT HUDSONALPHA DOT ORG)
   
   
 * DON JONES (DJONES AT COTTONINC DOT COM)
   
   
 * JEREMY SCHMUTZ (JSCHMUTZ AT HUDSONALPHA DOT ORG)




--------------------------------------------------------------------------------

The Upland Cottons Pangenome project conducted by the HudsonAlpha Institute for
Biotechnology was supported by the USDA-NIFA-AFRI grant (1028379) and genome
annotation was supported by the U.S. Department of Energy Joint Genome Institute
(JGI), funded by the Office of Science of the U.S. Department of Energy (DOE).
HudsonAlpha Institute for Biotechnology, Genome Sequencing Center | 601 Genome
Way NW, Building 601, Huntsville, AL 35806




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lbupcot.asreepga.development.svc.spin.nersc.org Open in urlscan Pro 128.55.206.102 Public Scan

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lbupcot.asreepga.development.svc.spin.nersc.org Open in urlscan Pro
128.55.206.102 Public Scan

Form analysis
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