Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.1.16.13

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.90582	0.578
27DAP/17DAP	0.91789	0.833
39DAP/27DAP	1.50295	0.184
41DAP/39DAP	0.78527	0.231
42DAP/41DAP	1.40195	0.419
43DAP/42DAP	1.12084	1
47DAP/43DAP	0.71176	0.263
52DAP/47DAP	0.87388	0.702
57DAP/52DAP	1.15987	0.946

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.859	0.032
17DAP/reference	0.96206	0.474
27DAP/reference	0.95741	0.385
39DAP/reference	0.82178	0.228
41DAP/reference	0.92782	0.201
42DAP/reference	0.85488	0.012
43DAP/reference	0.91523	0.17
47DAP/reference	0.86617	0.006
52DAP/reference	1.08202	0.476
57DAP/reference	1.21614	0.012

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.84852	0.402
27DAP/17DAP	1.49309	0.523
39DAP/27DAP	1.24111	0.163
41DAP/39DAP	0.89566	0.645
42DAP/41DAP	0.89839	0.399
43DAP/42DAP	0.84808	0.447
47DAP/43DAP	1.09492	0.997
52DAP/47DAP	1.11301	0.669
57DAP/52DAP	1.05684	0.971
57DAP/7DAP	0.77808

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.94163	0.246
17DAP/reference	1.03295	0.896
27DAP/reference	0.93197	0.2
39DAP/reference	1.17023	0.019
41DAP/reference	1.06877	0.577
42DAP/reference	1.19818	0.132
43DAP/reference	1.14305	0.105
47DAP/reference	0.99626	1
52DAP/reference	1.23218	0.139
57DAP/reference	1.14684	0.094

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.85282	0.029
17DAP/reference	0.75672	0.047
27DAP/reference	0.78886	0.053
39DAP/reference	0.84169	0.113
41DAP/reference	0.89751	0.127
42DAP/reference	0.75709	0.039
43DAP/reference	0.80119	0.066
47DAP/reference	0.92647	0.11
52DAP/reference	0.91153	0.055
57DAP/reference	0.83968	0.018

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.06185	0.676
17DAP/reference	0.97396	0.658
27DAP/reference	1.10389	0.284
39DAP/reference	0.98283	0.591
41DAP/reference	0.94412	0.264
42DAP/reference	0.96026	0.445
43DAP/reference	0.84568	0.116
47DAP/reference	0.94716	0.315
52DAP/reference	0.91801	0.433
57DAP/reference	0.87264	0.064

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.03687	0.966
26DAP/20DAP	1.17166	0.608
34DAP/26DAP	0.87143	0.693
51DAP/34DAP	1.01238	0.927
52DAP/51DAP	1.4036	0.089
53DAP/52DAP	1.29854	0.428
55DAP/53DAP	1.16478	0.764
57DAP/55DAP	0.9753	0.76
62DAP/57DAP	1.17074	0.723
68DAP/62DAP	1.3153	0.206
68DAP/14DAP	1.01783	0.958

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.87108	0.285

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	1.0044	0.835
Immature Eggplant/Mature Eggplant	1.14637
Ripe Pepper/Ripe Tomato	1.65338	1
Mature Eggplant/Ripe Tomato	0.95531	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	1.3138
12-2/M82	N/A	N/A
12-4/M82	1.07286	1
1-3/M82	N/A	N/A
2-1-1/M82	0.42285
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	1.9392
4-3-2/M82	1.45355	0.253
4-3/M82	N/A	N/A
5-3/M82	1.31527	0.572
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	0.95035	1
7-2/M82	N/A	N/A
9-3-2/M82	1.43156	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	2.58656
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	1.06965	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.97392	1
DC3000/delta hrp 6h	1.04499	1
DC3000/delta hrp 12h	0.92716	1
DC3000/delta hrp 24h	0.75682	0.04

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	N/A	N/A
DC3000 delta B/DC3000 delta AB	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.9067	0.328
Exp 36h	0.81353	0.41
Exp 60h	0.78305	0.586

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

hybridization	ratio	FDR (corrected p value)
self-self	0.97223	1
Var 0h	0.89948	0.933
Var 12h I row2-row1	1.0063	1
Var 12h NI row2-row1	0.84065	0.384
Var 36h I row2-row1	0.99742	1
Var 36h NI row2-row1	1.46437	0.482
Var 60h I row2-row1	0.69904
Var 60h NI row2-row1	1.0585	1
Time course 0hI-0hNI	0.92409	0.609
Time course 12hI-12hNI	0.99554	1
Time course 36hI-36hNI	0.87509	0.183
Time course 60hI-60hNI	0.328	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)	0.99595	0.931
transgenic ySAMdc/azygous control (breaker)	1.27677	0.162
transgenic ySAMdc/azygous control (red)	1.02516	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.00979	0.495

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.22618	0.237

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.73579	0.09
Manapal/WT (break)	1.2859	0.183
Manapal/WT (red)	2.40456	0.222