Tomato Functional Genomics Database (TFGD)

Expression of 1-1-8.4.1.14

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.00675	0.891
27DAP/17DAP	0.79419	0.499
39DAP/27DAP	0.8869	0.544
41DAP/39DAP	1.07995	0.772
42DAP/41DAP	1.04215	0.994
43DAP/42DAP	0.91043	0.858
47DAP/43DAP	1.22376	0.513
52DAP/47DAP	0.87502	0.683
57DAP/52DAP	0.92524	0.926

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.94914	0.254
17DAP/reference	0.94378	0.194
27DAP/reference	0.92962	0.187
39DAP/reference	0.86352	0.074
41DAP/reference	0.83464	0.154
42DAP/reference	0.88734	0.081
43DAP/reference	0.97601	0.653
47DAP/reference	0.99324	0.602
52DAP/reference	1.22205	0.02
57DAP/reference	1.06104	0.392

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.21122	0.365
27DAP/17DAP	1.05828	0.9
39DAP/27DAP	0.93522	0.55
41DAP/39DAP	1.13359	0.579
42DAP/41DAP	0.92637	0.576
43DAP/42DAP	0.91891	0.431
47DAP/43DAP	1.0513	0.901
52DAP/47DAP	1.00721	0.969
57DAP/52DAP	1.07928	0.951
57DAP/7DAP	1.06758	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.83869	0.095
17DAP/reference	0.97121	0.447
27DAP/reference	0.98286	0.53
39DAP/reference	1.03273	1
41DAP/reference	1.12484	0.491
42DAP/reference	1.2344	0.308
43DAP/reference	1.04111	0.83
47DAP/reference	1.03057	0.996
52DAP/reference	0.94443	0.332
57DAP/reference	1.00286	0.719

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.9766	0.72
17DAP/reference	0.9275	0.297
27DAP/reference	1.05642	0.781
39DAP/reference	1.13043	0.281
41DAP/reference	1.12331	0.309
42DAP/reference	1.01351	1
43DAP/reference	1.22858	0.202
47DAP/reference	1.03009	0.795
52DAP/reference	0.98764	0.576
57DAP/reference	0.90109	0.259

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.85761	0.065
17DAP/reference	1.04095	0.854
27DAP/reference	1.0153	1
39DAP/reference	0.98328	0.693
41DAP/reference	1.01906	0.961
42DAP/reference	1.13599	0.246
43DAP/reference	0.95245	0.416
47DAP/reference	1.00711	1
52DAP/reference	0.90469	0.31
57DAP/reference	1.32316	0.088

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.06362	0.966
26DAP/20DAP	1.15626	0.7
34DAP/26DAP	0.87691	0.811
51DAP/34DAP	1.22045	0.511
52DAP/51DAP	1.15163	0.873
53DAP/52DAP	1.56985	0.196
55DAP/53DAP	1.07635	0.938
57DAP/55DAP	1.00953	0.96
62DAP/57DAP	1.07681	0.868
68DAP/62DAP	1.21479	0.713
68DAP/14DAP	1.52456	0.328

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.4244	0.558

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.65385
Mature Green Tomato/Ripe Tomato	1.71	0.166
Immature Eggplant/Mature Eggplant	1.35797	0.174
Ripe Pepper/Ripe Tomato	1.4746	1
Mature Eggplant/Ripe Tomato	1.18496	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.11113	1
1-1-2/M82	1.06908	1
12-2/M82	1.09625	1
12-4/M82	1.34133
1-3/M82	0.92073	1
2-1-1/M82	1.24548
2-1/M82	1.21005
2-6/M82	0.91	1
3-2/M82	0.9649	1
4-1-1/M82	0.76989	0.863
4-1/M82	2.11314
4-3-2/M82	N/A	N/A
4-3/M82	1.09352	1
5-3/M82	0.94832	1
6-2/M82	0.73245	1
6-3/M82	0.98108	1
7-1/M82	0.88694	1
7-2/M82	0.74226	0.414
9-3-2/M82	0.76966

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.87192	0.321
IL2-6/WTpooled	1.16896
IL7-5/WTpooled	0.89505	1
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	0.6686	0.478
IL1-4/WTpooled	1.20701	1
WT/WTpooled	1.32183	0.789

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	1.07737	0.139

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.14335	0.57
DC3000/delta hrp 6h	0.97568	0.95
DC3000/delta hrp 12h	0.95049	1
DC3000/delta hrp 24h	0.99635	1

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.24826	1
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	0.97891	1
Exp 36h	0.87631	0.661
Exp 60h	1.03514	1

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

hybridization	ratio	FDR (corrected p value)
self-self	0.99544	1
Var 0h	1.12946	0.258
Var 12h I row2-row1	0.95072	0.514
Var 12h NI row2-row1	0.9967	0.443
Var 36h I row2-row1	1.06067	0.339
Var 36h NI row2-row1	0.67228	0.549
Var 60h I row2-row1	1.14027
Var 60h NI row2-row1	1.21051	0.904
Time course 0hI-0hNI	0.87591	0.247
Time course 12hI-12hNI	1.0442	0.811
Time course 36hI-36hNI	1.07555	0.19
Time course 60hI-60hNI	1.13003	0.137

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)	1.02495	0.571
transgenic ySAMdc/azygous control (breaker)	0.68206	0.139
transgenic ySAMdc/azygous control (red)	0.98586	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.03914	0.135

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.965	0.268

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.98723	1
Manapal/WT (break)	0.95601	1
Manapal/WT (red)	0.88455	0.242