Tools

Arachis Gene Expression

Arachis hypogaea Gene Expression: Tissues

Arachis Gene Atlas

Click for a description of the table, and credits and usage agreement

Arachis hypogaea gene expression: tissue by tissue comparisons
From this table, one can easily obtain the number of differentially expressed genes between any two tissues. There are two corresponding numbers for any tissue pair: The one above the diagonal is the number of genes that have significantly higher expression levels in the tissue presented in the row than that in the column, i.e., tissue-in-row > tissue-in-column. By contrast, the one below the diagonal is the number of genes that have significantly lower expression levels in the tissue presented in the column, i.e., tissue-in-column < tissue-in-row. For instance, in the case comparing lateral stem and main stem leaf, there are 21 genes that have a higher expression in lateral stem than in main stem leaf and there are 23 genes that have a lower expression in lateral stem than in main stem leaf. Clicking on the cell will result in a downloadable list of genes with their DESeq2 analysis results, including mean, log2FoldChange and adjusted-pvalue. In addition, gene GBrowse, sequence link and functional annotation are also included for further exploration.

Raw expression data is available from NCBI's GEO database, accession GSE71357

Credits: Reads were provided by Peggy Ozias-Akins and sequenced by Brian Scheffler and Mary Duke. Samples were harvested and prepared by Ye Chu. Read-mapping and differential expression analysis by Josh Clevenger and Wei Huang.

Citation: A Developmental Transcriptome Map for Allotetraploid Arachis hypogaea.. Josh Paul Clevenger, Ye Chu, Brian Scheffler and Peggy Ozias-Akins. (2016) Frontiers in Plant Biology. Also see associated Arachis hypogaea transcriptome assembly. Data for (GenBank)

Click for the list of tissue names

Tissues:

  • leaf 1::Lateral stem leaf
  • leaf 2::Mainstem leaf
  • leaf 3::Seedling leaf
  • veg shoot::Vegetative shoot tip
  • repr shoot::Reproductive shoot tip
  • root::Root
  • nodule::Nodule
  • perianth::Perianth
  • stamen::Stamen
  • pistil::Pistils
  • peg tip 1::Peg tip aerial
  • peg tip 2::Peg tip below soil
  • peg tip Pat. 1::Peg tip to fruit Pattee 1
  • fruit Pat. 1::Fruit Pattee 1
  • fruit Pat. 3::Fruit Pattee 3
  • pericarp Pat. 5::Pericarp Pattee 5
  • pericarp Pat. 6::Pericarp Pattee 6
  • seed Pat. 5::Seed Pattee 5
  • seed Pat. 6::Seed Pattee 6
  • seed Pat. 7::Seed Pattee 7
  • seed Pat. 8::Seed Pattee 8
  • seed Pat 10::Seed Pattee 10

Click for raw read counts download

Numbers in each cell of the following downloadable file are the raw read counts that are uniquely mapped on to Arachis hypogaea genome, produced by HTSeq.

Raw read counts in Arachis hypogaea RNAseq samples

Credits: Reads were provided by Peggy Ozias-Akins and sequenced by Brian Scheffler and Mary Duke. Samples were harvested and prepared by Ye Chu. Read-mapping and differential expression analysis by Josh Clevenger and Wei Huang.

Usage agreement: This analysis is under the same usage agreement (link is external) as for the genome assemblies and annotations. Please contact the authors, or inquire via Contact us, before using or citing this data.

leaf1leaf 2leaf 3veg shootrepr shootrootnoduleperianthstamenpistilpeg tip 1peg tip 2peg tip Pt 1Fruit Pt 1Fruit Pt 3PericarpPt6Pcarp Pt 6Seed Pt 5Seed Pt 6Seed Pt 7Seed Pt 8Seed Pt 10
leaf 1021698248774493791114611451966830879095119318187744897361063911552912988949539712410850
leaf 2230757040676390811114312421913148428038115068126705292921071311820833681528892660110438
leaf 3486307881744289901153311838788147908647112318556763896721054311562866185629255715811050
veg shoot81386786711508059931054412387464196745596791762901737586986231070334993411472736867687
repr shoot853474147441606061201131012442464299656313877165882264684293041138736863808548640909477
root111661049899847479688806995129707050108547599822247013137604958077042684966407550601710939
nodule976694199664848583024129011588882997769638104325522496562156469773877846994720548908877
perianth108291154910630118651112411003120930104276439105951239983939840111951116611089120531173512073960212948
stamen1043197929268557249476626112151043107749294529883978138548816375702452365738672152159627
pistil71488240738012507121341227714034920510055096351353880399234109821185712296126621247813018925113847
peg tip 19853889387917158693880431316412432421684060351442761931549068868049750979529181691612095
peg tip 21260312183114788241819375191291412924277010729151105184859550471927840754585019146772712030
peg tip Pt 17677759075246323598340787060881238655715317943240234922011704177172636730707850148355
Fruit Pt 176867204714923892276266768271047711077466774790231802431234246228612919350334717623
Fruit Pt 3102019650939262906351523783251208645718898364049861895680114123558035889654345219304
Pcarp Pt 5118841155210891910089815528923912599663499935995749418821301231040848882098737625811274
Pcarp Pt 61249712380116521058110294669710161123297259101517126786020293004185111209818972510168673412006
Seed Pt 587737838759831342607448491931181140009348527365816692192846997102903902267414577407
Seed Pt 68542763875773545300045678624116994649924158077666623223314968686389302601447506936
Seed Pt 78534757576574226388548857873115255123913064547512599626085133689785747661240654777
Seed Pt 8576152505388306429213811493389154091616547656227401526533405433051971156465701109
Seed Pt 108393766879855012578272877630108616691891581759057622452466633814893155123435929266410