Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.2.16.6

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.88799	0.395
27DAP/17DAP	0.54524	0.04
39DAP/27DAP	0.7396	0.399
41DAP/39DAP	0.7706	0.208
42DAP/41DAP	0.85476	1
43DAP/42DAP	1.52487	0.295
47DAP/43DAP	0.82869	0.473
52DAP/47DAP	0.84901	0.609
57DAP/52DAP	1.08714	0.996

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.28864	0.197
17DAP/reference	1.01089	0.717
27DAP/reference	0.91954	0.257
39DAP/reference	0.94839	0.174
41DAP/reference	1.03246	0.814
42DAP/reference	1.08179	0.174
43DAP/reference	0.64132	0.022
47DAP/reference	0.95951	0.418
52DAP/reference	0.98142	0.515
57DAP/reference	0.90459

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.88527	0.245
27DAP/17DAP	0.87089	0.339
39DAP/27DAP	0.61535	0.031
41DAP/39DAP	0.91349	0.822
42DAP/41DAP	1.14254	0.852
43DAP/42DAP	0.57541	0.022
47DAP/43DAP	0.80364	0.051
52DAP/47DAP	1.00032	0.962
57DAP/52DAP	0.77789	0.303
57DAP/7DAP	0.30578	0.219

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	2.70364	0.025
17DAP/reference	1.36641	0.007
27DAP/reference	0.8636	0.076
39DAP/reference	0.89883	0.23
41DAP/reference	0.66916	0.019
42DAP/reference	0.72378	0.024
43DAP/reference	0.70584	0.02
47DAP/reference	0.86692	0.222
52DAP/reference	0.76279	0.018
57DAP/reference	0.87846	0.069

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.24397	0.384
17DAP/reference	1.10404	0.176
27DAP/reference	0.90369	0.22
39DAP/reference	1.02417	1
41DAP/reference	0.96762	0.348
42DAP/reference	1.0245	0.934
43DAP/reference	0.9274	0.394
47DAP/reference	1.02096	0.795
52DAP/reference	0.95742	0.171
57DAP/reference	0.94383	0.144

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	3.30779	0.015
17DAP/reference	1.66672	0.212
27DAP/reference	1.18538	0.26
39DAP/reference	1.27137	0.015
41DAP/reference	0.95974	0.371
42DAP/reference	1.02368	0.816
43DAP/reference	1.06341	0.555
47DAP/reference	1.05245	0.585
52DAP/reference	1.10193	0.428
57DAP/reference	1.13684	0.522

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.91944	0.841
26DAP/20DAP	1.17094	0.477
34DAP/26DAP	0.99649	1
51DAP/34DAP	0.84887	0.323
52DAP/51DAP	0.95323	1
53DAP/52DAP	0.89107	0.323
55DAP/53DAP	0.51277	0.022
57DAP/55DAP	1.10444	0.71
62DAP/57DAP	1.21261	0.35
68DAP/62DAP	0.97802	0.834
68DAP/14DAP	0.8014	0.375

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.19791	0.019

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.08311	0.113
Mature Green Tomato/Ripe Tomato	10.1255	0.019
Immature Eggplant/Mature Eggplant	0.69323	0.062
Ripe Pepper/Ripe Tomato	6.17248	1
Mature Eggplant/Ripe Tomato	9.22159	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	2.5658
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	0.5158
7-2/M82	N/A	N/A
9-3-2/M82	2.55418	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
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	N/A	N/A
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	0.93428	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.94039	1
DC3000/delta hrp 6h	0.91488	0.95
DC3000/delta hrp 12h	1.15079	1
DC3000/delta hrp 24h	0.49076	0.034

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.64223	0.024
DC3000 delta B/DC3000 delta AB	0.59196	0.02

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.96164	1
Exp 36h	0.76397	0.397
Exp 60h	0.65827	0.259

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

hybridization	ratio	FDR (corrected p value)
self-self	1.02268	1
Var 0h	1.23864	0.782
Var 12h I row2-row1	0.83495	0.338
Var 12h NI row2-row1	0.95175	0.82
Var 36h I row2-row1	0.77729	1
Var 36h NI row2-row1	1.14879	0.276
Var 60h I row2-row1	1.03563	1
Var 60h NI row2-row1	0.98212	1
Time course 0hI-0hNI	0.9791	0.934
Time course 12hI-12hNI	1.08929	0.445
Time course 36hI-36hNI	1.01309	1
Time course 60hI-60hNI	0.20845	0.006

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)	1.01065	0.748
transgenic ySAMdc/azygous control (breaker)	1.06341	1
transgenic ySAMdc/azygous control (red)	1.05077	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.95476	0.087

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.96528	0.237

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	2.44335	0.083
Manapal/WT (break)	2.34887	0.14
Manapal/WT (red)	1.84306	0.164