Manual

CATchUP_manual.pdf

NGS samples used for the analysis

Species Number of runs Link
Arabidopsis thaliana 1,360 arabidopsis_thaliana_run.txt
Oryza sativa 454 oryza_sativa_run.txt
Solanum lycopersicum 817 solanum_lycopersicum_run.txt
Sorghum bicolor 112 sorghum_bicolor_run.txt
Vitis vinifera 107 vitis_vinifera_run.txt
Medicago truncatula 68 medicago_truncatula_run.txt
Solanum tuberosum 72 solanum_tuberosum_run.txt
Glycine max 693 glycine_max_run.txt
Total 3,683

Statistics for the candidate genes showing spatiotemporal expression profiles

Species The number of transcripts that was used for this analysis The number of candidate transcripts (Δdmax ≥ 0.3)
Arabidopsis thaliana 38,978 8,356
Oryza sativa 52,194 15,644
Solanum lycopersicum 33,624 5,690
Sorghum bicolor 38,922 7,084
Vitis vinifera 53,795 6,062
Medicago truncatula 60,566 6,887
Solanum tuberosum 21,987 5,114
Glycine max 88,502 15,644

Detection of genes showing spatiotemporal expression

(1) A gene was removed unless the maximum FPKM value of the gene was more than 10.

(2) Each FPKM was divided by the maximum FPKM value of the gene.

(3) Experimental samples were rearranged in ascending order of the normalized FPKM values (a row vector g with n elements, g = (g1, g2, g3, ···, gn)).

(4) The differences ∆di between two neighboring elements, namely ∆di = gi+1 - gi (i = 1~(n-1)) were calculated.

(5) The maximum value ∆dmax was obtained among all ∆di values.

(6) we selected genes as candidates for spatiotemporally expressed genes using the threshold value ∆dmax ≥ 0.3.

Contact

Kentaro Yano