AI logo

NASCArrays

start again, selection, spot history, gene swinger, two gene scatterplot, digital northern, bulk gene download, tutorial, help, Affymetrix site, NASC home

Welcome to NASCArrays.

NASCArrays is the Nottingham Arabidopsis Stock Centre's microarray database. Currently most of the data is for Arabidopsis thaliana experiments run by the NASC Affymetrix Facility. There are also experiments from other species, and experiments run by other centres too. If you would like to see your data in this database, consult the donation page.

To navigate around this website, use the orange menus at the top of every page. "start again" will always bring you back to this page. To get the most out of this website, why not follow the tutorial (available from the "tutorial" link at the top of this page). Full documentation for all of the features on the website is available from the "help" section.

If you want to get large amounts of data from the database, you need AffyWatch! Affywatch is a CD subscription service, that for £50 will allow you quick access to all of the data on this website. Click here for more information.

For more information on NASC's Affymetrix service, you can visit our Affymetrix site by choosing Affymetrix site from the orange menu at the top, or by using Help.

There are three main ways into the data:

1) Search

Experiment Search

You can search for keywords to help you identify experiments you might be interested in.

Search for:

Hints

  • Type in as many words as you like
  • Type in words that you think are likely to be specific to what you are looking for rather than used a lot
  • Consider words as "keywords" not phrases.

Search by NASCArrays Reference Number

Enter Reference Number (e.g. 343): NASCARRAYS-
(The number after the "NASCARRAYS-" prefix is synonymous with the Experiment ID.)

Slide Search

This search allows you to search for slides that match your criteria. Type in terms you wish to search for, and the fields you wish to search for them in, below.

  contains
AND contains
AND contains
AND contains
AND contains

2) Use a data-mining tool

There are currently the following data mining tools available. All of these tools allow you to type in a gene(s) of interest, and identify experiments or slides that you might be interested in. Click on the links to use.

  • Spot History: This tool allows you to see the pattern of gene expression over all slides in the database. Easily identify slides (and therefore experimental treatments) where genes are highly, lowly, or unusually expressed
  • Two gene scatter plot: This tool allows you to see the pattern of gene expression over all slides for two genes as a scatter plot. If you are interested in two genes, you can find out if they act in tandem, and highlight slides (and therefore experimental conditions) where these two genes behave in an unusual manner.
  • Gene Swinger: If you have a gene of interest, this tool will show you which experiment the gene expression varied most
  • Bulk Gene Download: This tool allows you to download the expression of a list of genes over all experiments. You can get all genes over all experiments (the entire database!) from the Super Bulk Gene Download
    • .

3) Treeview

The treeview allows you to browse the list of experiments. We have categorised all the experiments using various criteria.

To work the treeview, click on the categories. The branches below will expand, showing you all of the experiments in that category. To visit an experiment you are interested in, click on the link and you will be taken to a page about that experiment. One experiment can appear under more than one branch of the tree.

+folder imageDate view experiments sorted by date
+folder imageApril 2009
+folder imageMarch 2009
+folder imageJanuary 2009
+folder imageNovember 2008
+folder imageSeptember 2008
+folder imageAugust 2008
+folder imageJuly 2008
+folder imageJune 2008
+folder imageApril 2008
+folder imageFebruary 2008
+folder imageJanuary 2008
+folder imageNovember 2007
+folder imageAugust 2007
+folder imageJuly 2007
+folder imageMay 2007
+folder imageApril 2007
+folder imageFebruary 2007
+folder imageJanuary 2007
+folder imageDecember 2006
+folder imageOctober 2006
+folder imageSeptember 2006
+folder imageJune 2006
+folder imageMay 2006
+folder imageApril 2006
+folder imageMarch 2006
+folder imageFebruary 2006
+folder imageJanuary 2006
+folder imageDecember 2005
+folder imageNovember 2005
+folder imageOctober 2005
+folder imageSeptember 2005
+folder imageAugust 2005
+folder imageJuly 2005
+folder imageJune 2005
+folder imageApril 2005
+folder imageMarch 2005
+folder imageFebruary 2005
+folder imageJanuary 2005
+folder imageDecember 2004
+folder imageNovember 2004
+folder imageOctober 2004
+folder imageAugust 2004
+folder imageJuly 2004
+folder imageJune 2004
+folder imageApril 2004
+folder imageMarch 2004
+folder imageJanuary 2004
+folder imageNovember 2003
+folder imageOctober 2003
+folder imageAugust 2003
+folder imageJuly 2003
+folder imageJune 2003
+folder imageMay 2003
+folder imageApril 2003
+folder imageMarch 2003
+folder imageJanuary 2003
+folder imageDecember 2002
+folder imageNovember 2002
+folder imageOctober 2002
+folder imageSeptember 2002
+folder imageAugust 2002
+folder imageJuly 2002
+folder imageJune 2001
-folder imageMGED Classification classifications based on the MGED ontology
+folder imageExperimentDesignType automatic classification on the type of experiments based on MGED ontology
+folder imageBiologicalProperty experiments where an intrinsic characteristic of an organism(s) or biological system is examined
+folder imagedevelopment_or_differentiation_design
+folder imageorganism_part_comparison_design
+folder imagestrain_or_line_design
+folder imageMethodologicalDesign experiments investigating differences caused by application of protocols. e.g. timecourses
+folder imagetime_series_design
+folder imagePerturbationalDesign experiments where the organism(s) are treated or manipulated or modified (all treatment experiments)
+folder imagecompound_treatment_design
+folder imagegenetic_modification_design
+folder imagegrowth_condition_design
+folder imagepathogenicity_design
+folder imagestimulus_or_stress_design
+folder imageExperimentalFactorCategory automatic classification on the factors of experiments based on MGED ontology
+folder imageBiologicalFactorCategory factors to do with properties of the plant, its treatment, or its growth.
+folder imageAction procedures used during treatment
+folder imageAtomicAction simple treatments
+folder imagechange_light
+folder imagechange_temperature
+folder imageconcentrate
+folder imageComplexAction complex treatments
+folder imagecompound_based_treatment
+folder imagegrow
+folder imageinfect
+folder imageirradiate
+folder imagestarvation
+folder imageBioMaterialCharacteristicCategory factors to do with specific features of the organism e.g. strain or line, or developmental stage
+folder imageage
+folder imagedevelopmental_stage
+folder imagegenetic_variation
+folder imageorganism
+folder imageorganism_part
+folder imagestrain_or_line
+folder imageBioMaterialCharacteristics more factors to do with specific features of the organism e.g. strain or line, or developmental stage
+folder imageEnvironmentalHistory
+folder imageGrowthCondition
+folder imageLight
+folder imageNutrients
+folder imageTemperature
+folder imageGeneticModification knockout/in vs wildtype etc.
+folder imagegene_knock_out
+folder imageinduced_mutation
+folder imageEnvironmentalFactorCategory atmosphere, media, water
+folder imageatmosphere
+folder imagemedia
+folder imagewater
+folder imageAlphabetical by person in alphabetical order
+folder image
+folder imageA
+folder imageB
+folder imageC
+folder imageD
+folder imageE
+folder imageF
+folder imageG
+folder imageH
+folder imageI
+folder imageJ
+folder imageK
+folder imageL
+folder imageM
+folder imageN
+folder imageO
+folder imageP
+folder imageR
+folder imageS
+folder imageT
+folder imageU
+folder imageV
+folder imageW
+folder imageX
+folder imageY
+folder imageZ
+folder imageAtGenExpress Project the AtGenExpress experiments, laid out by section
+folder imageDevelopmental Stage
+folder imageGrowth Condition Treatments
+folder imagePathogen Infection
+folder imageStress Series
+folder imageHormone Treatments
+folder imageAFGC data a set of two-colour data from the (now-finished) AFGC project

This page has recently changed. If you would like to look at the old index page, click here,

Problems? Comments? Suggestions? Contact the Affymetrix Team