bioops / legume_network

conserved and specific legume co-expression networks

Conserved and specific legume co-expression network

summary

soybean, medicago and lotus

bla bla

dataset

all data file were stored in ./data directory.

soybean (williams 82):

• expression data (microarray)
• platform: Affymetrix GeneChip Soybean Genome Array
• MetAffx annotation
• raw data 1
• paper 1
• samples 1: 4*4 leaf
• raw data 2
• paper 2: NA
• samples 2: 13*2 seed
• genome assembly and annotation: December 2008 (JGI Glyma1 v1.01)

medicago

• expression data (microarray)
• platform: Affymetrix GeneChip Medicago Genome Array
• NetAffx annotation
• raw data
• paper
• samples: 18*3=54
• genome assembly and annotation: Medicago.org Mt3.0 (Although the current version is 3.5, Affymetrix was using 3.0 version to annotate this microarray platform)

lotus

• expression data (microarray)
• platform: Affymetrix Custom Array - Lotus1a520343
• NetAffx annotation: NA
• ArrayDesign XML
• raw data
• paper: NA
• samples: 15*3=45
• genome assembly and annotation: Lotus japonicus genome assembly build 2.5

main workflow

• data preparation. (check ./prepare directory for more details)
• conserved network identification
  • method 1: network comparison ( check ./net directory for more details)
  • method 2: meta-analysis
• GO enrichment analysis