Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.3.18.21

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.53205	0.016
27DAP/17DAP	1.32999	0.742
39DAP/27DAP	1.47524	0.38
41DAP/39DAP	0.9959	0.876
42DAP/41DAP	0.55981	0.262
43DAP/42DAP	0.86109	0.708
47DAP/43DAP	0.7052	0.216
52DAP/47DAP	1.5442	0.528
57DAP/52DAP	0.94699	0.932

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.83844	0.063
17DAP/reference	0.97102	0.597
27DAP/reference	0.88227	0.182
39DAP/reference	0.8603	0.088
41DAP/reference	0.80806	0.013
42DAP/reference	0.90488	0.018
43DAP/reference	0.95578	0.576
47DAP/reference	0.90324	0.018
52DAP/reference	0.94828	0.25
57DAP/reference	1.03221	0.927

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.36831	0.536
27DAP/17DAP	0.8449	0.227
39DAP/27DAP	0.95228	0.692
41DAP/39DAP	1.55855	0.017
42DAP/41DAP	0.82812	0.125
43DAP/42DAP	0.69514	0.025
47DAP/43DAP	0.9962	0.985
52DAP/47DAP	1.21596	0.492
57DAP/52DAP	1.14565	0.899
57DAP/7DAP	0.75288	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.40862	0.085
17DAP/reference	1.42653	0.019
27DAP/reference	1.39755	0.049
39DAP/reference	1.42039	0.048
41DAP/reference	1.37256	0.022
42DAP/reference	1.4105	0.046
43DAP/reference	1.49785	0.007
47DAP/reference	1.3125	0.055
52DAP/reference	1.49885	0.009
57DAP/reference	1.35248	0.082

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.94585	0.518
17DAP/reference	1.08871	0.873
27DAP/reference	0.98422	0.554
39DAP/reference	0.98479	0.497
41DAP/reference	0.95685	0.277
42DAP/reference	0.90013	0.15
43DAP/reference	0.87689	0.181
47DAP/reference	0.95338	0.311
52DAP/reference	1.05505	0.559
57DAP/reference	1.02598	0.64

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.10537	0.244
17DAP/reference	1.00404	0.81
27DAP/reference	1.3571	0.038
39DAP/reference	1.29941	0.018
41DAP/reference	1.24316	0.05
42DAP/reference	1.09499	0.566
43DAP/reference	1.06544	0.855
47DAP/reference	0.97249	0.465
52DAP/reference	1.339	0.369
57DAP/reference	0.97848	0.602

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.99364	1
26DAP/20DAP	1.05686	1
34DAP/26DAP	0.80848	0.596
51DAP/34DAP	1.60067	0.637
52DAP/51DAP	1.09463	0.954
53DAP/52DAP	0.97314	0.862
55DAP/53DAP	1.33304	0.622
57DAP/55DAP	1.20957	0.935
62DAP/57DAP	1.08319	1
68DAP/62DAP	1.49816	0.057
68DAP/14DAP	1.43785	0.436

Experiment: Tomato (breaker-stage) vs. Pepper (breaker-stage)

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.29133	0.081

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.31676	0.107
Mature Green Tomato/Ripe Tomato	1.16775	0.331
Immature Eggplant/Mature Eggplant	2.30618	0.05
Ripe Pepper/Ripe Tomato	3.92722	1
Mature Eggplant/Ripe Tomato	2.31708	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	N/A	N/A
12-2/M82	N/A	N/A
12-4/M82	N/A	N/A
1-3/M82	N/A	N/A
2-1-1/M82	N/A	N/A
2-1/M82	N/A	N/A
2-6/M82	N/A	N/A
3-2/M82	N/A	N/A
4-1-1/M82	N/A	N/A
4-1/M82	N/A	N/A
4-3-2/M82	N/A	N/A
4-3/M82	N/A	N/A
5-3/M82	N/A	N/A
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	N/A	N/A
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.79364
IL2-6/WTpooled	1.17011	0.531
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.86489
IL12-4/WTpooled	0.85064	1
IL1-4/WTpooled	1.02073	1
WT/WTpooled	1.13864	0.777

Experiment: Transcriptional changes determined by expression of the Xanthomonas AvrRxv effector in resistant tomato plants

hybridization	ratio	FDR (corrected p value)
10 h post inoculation	0.97726	1

Experiment: Time course of DC3000 vs delta hrp on tomato Prf-3

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.26686	0.875
DC3000/delta hrp 6h	1.25827	1
DC3000/delta hrp 12h	0.91509	1
DC3000/delta hrp 24h	3.72435	0.025

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.44481	0.042
DC3000 delta B/DC3000 delta AB	1.41143	0.083

Experiment: Matt's wild cherry tomato vs. Phytophthora infestans

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.27616	1
Exp 36h	0.98841	0.943
Exp 60h	1.24601	0.399

Experiment: Gene expression profiling of infection of tomato by Phytophthora infestans in the field

hybridization	ratio	FDR (corrected p value)
self-self	1.08726	1
Var 0h	1.00733	1
Var 12h I row2-row1	1.13405	0.379
Var 12h NI row2-row1	1.13008	0.34
Var 36h I row2-row1	1.16504	1
Var 36h NI row2-row1	0.8426	0.645
Var 60h I row2-row1	0.6618	0.374
Var 60h NI row2-row1	0.89973	0.69
Time course 0hI-0hNI	1.17761	0.151
Time course 12hI-12hNI	0.96715	0.802
Time course 36hI-36hNI	1.37403	0.006
Time course 60hI-60hNI	2.62104	0.008

Experiment: Transcriptional profiling of the tomato fruit pericarp tissue: fruits overexpressing yeast ySAMdc gene and controls

hybridization	ratio	FDR (corrected p value)
transgenic ySAMdc/azygous control (mature green)	0.88727	0.428
transgenic ySAMdc/azygous control (breaker)	0.78056	0.251
transgenic ySAMdc/azygous control (red)	1.03938	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.08257	0.077

Experiment: Microarray Analysis on Salt Stress Affected Genes in Tomato Seedlings

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.83642	0.238

Experiment: Transcriptional Profiling of high pigment-2dg Tomato Mutant Fruit

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.83353	1
Manapal/WT (break)	1.00379	1
Manapal/WT (red)	0.89885	0.424