Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.2.3.16

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.00573	0.919
27DAP/17DAP	1.45035	0.742
39DAP/27DAP	2.23895	0.416
41DAP/39DAP	1.07675	0.785
42DAP/41DAP	1.32903	0.193
43DAP/42DAP	0.87379	0.743
47DAP/43DAP	1.23729	0.448
52DAP/47DAP	1.0493	0.938
57DAP/52DAP	1.40876	0.935

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.86361	0.172
17DAP/reference	0.73456	0.007
27DAP/reference	0.78789	0.011
39DAP/reference	0.87357	0.083
41DAP/reference	0.83369	0.154
42DAP/reference	0.92828	0.017
43DAP/reference	0.64012
47DAP/reference	0.95898	0.392
52DAP/reference	1.09121	0.079
57DAP/reference	0.43731	0.008

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.75834	0.311
27DAP/17DAP	1.16592	0.598
39DAP/27DAP	1.15945	0.541
41DAP/39DAP	1.39096	0.276
42DAP/41DAP	1.01813	0.939
43DAP/42DAP	0.82543	0.28
47DAP/43DAP	1.43821	0.025
52DAP/47DAP	0.76971	0.117
57DAP/52DAP	0.91654	0.632
57DAP/7DAP	1.45473	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.1122	0.511
17DAP/reference	1.3368	0.011
27DAP/reference	1.35503	0.01
39DAP/reference	1.47708	0.062
41DAP/reference	1.56757	0.05
42DAP/reference	1.86849	0.046
43DAP/reference	1.62902	0.008
47DAP/reference	1.23744	0.071
52DAP/reference	1.60447	0.019
57DAP/reference	1.50341	0.029

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.84695	0.051
17DAP/reference	0.76811	0.014
27DAP/reference	1.03561	0.726
39DAP/reference	1.21578	0.182
41DAP/reference	1.08621	0.382
42DAP/reference	1.01105	1
43DAP/reference	1.01082	0.875
47DAP/reference	1.00504	1
52DAP/reference	1.06502	0.559
57DAP/reference	0.91096	0.243

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.23642	0.09
17DAP/reference	1.13074	0.545
27DAP/reference	1.2043	0.07
39DAP/reference	1.37884	0.033
41DAP/reference	1.59046	0.022
42DAP/reference	1.41639	0.028
43DAP/reference	1.40612	0.028
47DAP/reference	1.05385	0.76
52DAP/reference	1.33356	0.172
57DAP/reference	1.55191	0.015

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.16261	0.966
26DAP/20DAP	1.31267	0.404
34DAP/26DAP	0.4685	0.186
51DAP/34DAP	1.41236	0.365
52DAP/51DAP	0.64539	0.079
53DAP/52DAP	1.00845	0.96
55DAP/53DAP	1.11171	0.855
57DAP/55DAP	0.84093
62DAP/57DAP	0.95066	0.994
68DAP/62DAP	1.6689	0.051
68DAP/14DAP	2.21833	0.03

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.56695	0.024

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.45899	0.017
Immature Eggplant/Mature Eggplant	4.52583	0.05
Ripe Pepper/Ripe Tomato	0.55161	0.224
Mature Eggplant/Ripe Tomato	0.21819	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.07024	1
1-1-2/M82	0.63221
12-2/M82	0.61722
12-4/M82	1.4763
1-3/M82	1.65065
2-1-1/M82	N/A	N/A
2-1/M82	N/A	N/A
2-6/M82	0.86982
3-2/M82	N/A	N/A
4-1-1/M82	N/A	N/A
4-1/M82	1.54915
4-3-2/M82	2.23813
4-3/M82	N/A	N/A
5-3/M82	1.0886
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	1.09456
7-2/M82	0.96831
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.7249
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	N/A	N/A
IL1-4/WTpooled	0.86647
WT/WTpooled	N/A	N/A

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	1.55848	0.479

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.94361	1
DC3000/delta hrp 6h	1.59003	0.857
DC3000/delta hrp 12h	1.19065	1
DC3000/delta hrp 24h	1.27548	0.453

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	2.01887
DC3000 delta B/DC3000 delta AB	2.34611	0.079

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.36662	0.254
Exp 36h	1.4639	0.693
Exp 60h	1.56909	0.563

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

hybridization	ratio	FDR (corrected p value)
self-self	1.21729
Var 0h	1.44893	0.782
Var 12h I row2-row1	1.03843	1
Var 12h NI row2-row1	1.16085	0.235
Var 36h I row2-row1	1.19187	0.742
Var 36h NI row2-row1	0.87279	0.378
Var 60h I row2-row1	0.87394	0.832
Var 60h NI row2-row1	0.56859	0.292
Time course 0hI-0hNI	1.33604	0.323
Time course 12hI-12hNI	2.18993	0.015
Time course 36hI-36hNI	5.62018	0.004
Time course 60hI-60hNI	21.3419	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)	0.65303	0.26
transgenic ySAMdc/azygous control (breaker)	0.46915	0.134
transgenic ySAMdc/azygous control (red)	0.87977	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.16341	0.047

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.33853	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.90193	1
Manapal/WT (break)	0.91873	1
Manapal/WT (red)	0.49459	0.36