Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.2.17.14

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.79607	0.137
27DAP/17DAP	1.3502	0.798
39DAP/27DAP	1.42932	1
41DAP/39DAP	1.93085	0.185
42DAP/41DAP	3.22439	0.021
43DAP/42DAP	3.06316	0.491
47DAP/43DAP	1.03191	0.999
52DAP/47DAP	0.54632	0.072
57DAP/52DAP	1.63404	0.892

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.3054	0.48
17DAP/reference	0.9813	0.737
27DAP/reference	1.31954	0.252
39DAP/reference	1.05276	0.679
41DAP/reference	0.98825	0.814
42DAP/reference	1.30824	0.014
43DAP/reference	0.98254	0.728
47DAP/reference	1.29377	0.081
52DAP/reference	1.92814	0.011
57DAP/reference	1.48777	0.011

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.90276	0.509
27DAP/17DAP	0.99087	0.943
39DAP/27DAP	1.25098	0.151
41DAP/39DAP	0.81067	0.412
42DAP/41DAP	1.33411	0.172
43DAP/42DAP	1.63601	0.018
47DAP/43DAP	1.10088	0.857
52DAP/47DAP	0.83391	0.334
57DAP/52DAP	0.95748	0.726
57DAP/7DAP	1.22285	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.9033	0.296
17DAP/reference	0.76139	0.012
27DAP/reference	0.72355	0.01
39DAP/reference	0.90214	0.146
41DAP/reference	0.8488	0.223
42DAP/reference	0.70769	0.017
43DAP/reference	0.99813	0.665
47DAP/reference	0.98163	0.671
52DAP/reference	0.80029	0.09
57DAP/reference	0.83165	0.032

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.07855	0.93
17DAP/reference	0.88819	0.245
27DAP/reference	0.98793	0.686
39DAP/reference	1.18432	0.588
41DAP/reference	1.31066	0.031
42DAP/reference	1.23351	0.18
43DAP/reference	0.91631	0.277
47DAP/reference	1.2362	0.076
52DAP/reference	1.21854	0.393
57DAP/reference	0.95072	0.519

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.83513	0.038
17DAP/reference	0.90256	0.3
27DAP/reference	0.7385	0.035
39DAP/reference	0.80469	0.046
41DAP/reference	0.97202	0.56
42DAP/reference	0.87328	0.059
43DAP/reference	1.01697	0.685
47DAP/reference	1.34518	0.133
52DAP/reference	0.88293	0.455
57DAP/reference	1.44906	0.041

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.90941	1
26DAP/20DAP	0.82976	0.512
34DAP/26DAP	2.04971	0.819
51DAP/34DAP	1.7566	0.565
52DAP/51DAP	1.9377
53DAP/52DAP	0.9668	0.891
55DAP/53DAP	1.85497	0.252
57DAP/55DAP	0.85775	0.386
62DAP/57DAP	1.37143	0.445
68DAP/62DAP	2.18609	0.066
68DAP/14DAP	4.11203	0.366

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	2.38073	0.087

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.38132	0.017
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	N/A	N/A
Mature Eggplant/Ripe Tomato	N/A	N/A

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	1.02385
12-2/M82	N/A	N/A
12-4/M82	1.85907
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	1.08025
4-3-2/M82	1.03612	1
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	0.93011
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	N/A	N/A
IL2-6/WTpooled	1.06292	0.788
IL7-5/WTpooled	0.5466
IL7-3/WTpooled	0.90987	1
IL12-4/WTpooled	0.97823	1
IL1-4/WTpooled	0.99924	1
WT/WTpooled	1.00644	1

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	0.89288	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.05386	1
DC3000/delta hrp 6h	N/A	N/A
DC3000/delta hrp 12h	1.00742	1
DC3000/delta hrp 24h	0.40956	0.034

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.2063	0.598
DC3000 delta B/DC3000 delta AB	2.074	0.079

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.22508	1
Exp 36h	N/A	N/A
Exp 60h	1.2335	0.22

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

hybridization	ratio	FDR (corrected p value)
self-self	0.97714	1
Var 0h	1.45269	0.936
Var 12h I row2-row1	0.94344	0.627
Var 12h NI row2-row1	1.37353	0.34
Var 36h I row2-row1	0.92582	1
Var 36h NI row2-row1	0.99332	0.852
Var 60h I row2-row1	0.62348	0.374
Var 60h NI row2-row1	0.92954	1
Time course 0hI-0hNI	1.19786	0.451
Time course 12hI-12hNI	0.84914	0.163
Time course 36hI-36hNI	1.30523	0.128
Time course 60hI-60hNI	2.29118	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)	0.91383	0.662
transgenic ySAMdc/azygous control (breaker)	0.79283	0.251
transgenic ySAMdc/azygous control (red)	0.92337	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.89875	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.11062	0.307
Manapal/WT (break)	1.04992	1
Manapal/WT (red)	1.03735	1