How to download

Method

• Union Coexpression
• [u22] (Gene pairs with Xxx-r and Xxx-m: mean(z(Xxx-r), z(Xxx-m)). Gene pairs only with Xxx-r: (0.5)^0.2 * z(Xxx-r)) → z
• [u21] (Gene pairs with Xxx-r and Xxx-m: mean(LS(Xxx-r), LS(Xxx-m)). Gene pairs only with Xxx-r: Linear regression of Xxx-u on Xxx-r) → z
• [u20] Gene pairs with Xxx-r and Xxx-m: mean(LS(Xxx-r), LS(Xxx-m)). Gene pairs only with Xxx-r: Linear regression of Xxx-u on Xxx-r
• RNAseq Coexpression
• [r21] Matataki → filter(s>2M, g>mean30) → log2(x+0.125) → ComBat → zero-centering → PCA → Subagging (50, PCC → MR → logit) → LS → z-score
• [r20] Matataki → filter(s>2M, g>mean30) → log2(x+0.125) → ComBat → zero-centering → PCA → Subagging (30%, PCC → MR → logit) → LS
• [r17c] Matataki → filter(s>2M, g>mean30) → log2(x+0.125) → ComBat → batch-zero-centering → Bagging (PCC → MR → logit) → MR
• [r17b] Matataki → filter(s>2M, g>mean30) → log2(x+0.125) → ComBat → Quantile → Bagging (PCC → MR → logit) → MR
• [r17a] Matataki → filter(s>2M, g>mean30) → log2(x+0.125) → ComBat → Quantile → PCC → MR
• [r15] Bowtie → filter(s > 10M, g > max100) → log2(x+0.125) → Quantile → batch-zero-centering → PCC → MR
• [r13] Bowtie → filter(s > 5M, g > max100) → log2(x+1) → Quantile → batch-zero-centering → PCC → MR
• Microarray Coexpression
• [m21] RMA → ComBat → zero-centering → PCA → Subagging (50, PCC → MR → logit) → LS → z-score
• [m20] RMA → ComBat → zero-centering → PCA → Subagging (30%, PCC → MR → logit) → LS
• [m17b] RMA → ComBat → batch-zero-centering → Bagging (PCC → MR → logit) → MR
• [m17a] RMA → ComBat → batch-zero-centering → PCC → MR
• [m08] RMA → batch-zero-centering → weighted PCC → MR
• [m06] RMA → batch-zero-centering → weighted PCC

Data format (tab-deliminated)

Ath-m.c8-0

• File name; Entrez Gene ID of the guide gene.
• Column 1; Entrez Gene ID of an opposite gene of coexpression.
• Column 2; LS (Logit Score). Lines are sorted by this value.

Ath-m.c6-0

• File name; Entrez Gene ID of the guide gene.
• Column 1; Entrez Gene ID of an opposite gene of coexpression.
• Column 2; MR (Mutual Rank). Lines are sorted by this value.
• Column 3; Pearson's Correlation Coefficient (PCC). Deprecated. In detail, please see our publication (Obayashi and Kinoshita, 2009).

[How to calculate the co-expressed gene table]

Download and Unzip

 
 # for Arabidopsis
 $ wget --content-disposition http://atted.jp/download/Ath-m.c8-0/coex
 $ md5 Ath-m.v19-11.G20819-S12686.combat_pca_subagging.ls.d.zip
 $ unzip Ath-m.v19-11.G20819-S12686.combat_pca_subagging.ls.d.zip