Tomato Functional Genomics Database (TFGD)

Expression of 1-1-4.3.13.14

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.37829	0.428
27DAP/17DAP	0.81432	0.392
39DAP/27DAP	1.64177	0.078
41DAP/39DAP	0.74399	0.185
42DAP/41DAP	0.84638	1
43DAP/42DAP	0.87791	0.736
47DAP/43DAP	0.48206	0.049
52DAP/47DAP	1.29432	0.601
57DAP/52DAP	0.75441	0.44

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.31307	0.023
17DAP/reference	1.10428	0.117
27DAP/reference	1.06747	0.194
39DAP/reference	1.06394	0.277
41DAP/reference	1.0028	1
42DAP/reference	0.95847	0.202
43DAP/reference	0.91944	0.148
47DAP/reference	0.93469	0.161
52DAP/reference	0.98159	0.546
57DAP/reference	1.1552	0.041

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.63214	0.038
27DAP/17DAP	0.71694	0.099
39DAP/27DAP	0.93426	0.488
41DAP/39DAP	1.24893	0.807
42DAP/41DAP	0.96641	0.704
43DAP/42DAP	0.60375	0.022
47DAP/43DAP	0.87351	0.192
52DAP/47DAP	0.87034	0.378
57DAP/52DAP	0.8057	0.252
57DAP/7DAP	0.81629	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.01282	0.758
17DAP/reference	0.9044	0.082
27DAP/reference	0.96139	0.375
39DAP/reference	0.90276	0.073
41DAP/reference	0.99663	0.646
42DAP/reference	0.82166	0.011
43DAP/reference	0.87446	0.018
47DAP/reference	1.15448	0.404
52DAP/reference	0.82737	0.053
57DAP/reference	0.76605	0.008

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.13199	0.443
17DAP/reference	1.22842	0.176
27DAP/reference	1.44614	0.133
39DAP/reference	1.31156	0.03
41DAP/reference	1.47801	0.046
42DAP/reference	1.06564	0.359
43DAP/reference	1.11178	0.617
47DAP/reference	0.98991	0.609
52DAP/reference	1.11943	0.223
57DAP/reference	0.89444	0.243

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.91434	0.214
17DAP/reference	1.02133	0.746
27DAP/reference	0.89722	0.126
39DAP/reference	0.94706	0.393
41DAP/reference	0.94094	0.331
42DAP/reference	0.8754	0.059
43DAP/reference	0.89796	0.092
47DAP/reference	0.76669	0.026
52DAP/reference	0.71567	0.071
57DAP/reference	0.97088	0.516

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.76714	0.89
26DAP/20DAP	0.66309
34DAP/26DAP	1.30713	1
51DAP/34DAP	N/A	N/A
52DAP/51DAP	0.826
53DAP/52DAP	1.02178	1
55DAP/53DAP	1.02598	0.948
57DAP/55DAP	4.03328	0.71
62DAP/57DAP	0.91167	0.871
68DAP/62DAP	0.99849	0.914
68DAP/14DAP	1.26438	0.487

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	3.64111	0.015

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	6.59603	0.015
Immature Eggplant/Mature Eggplant	0.53582	0.057
Ripe Pepper/Ripe Tomato	0.07266	0.224
Mature Eggplant/Ripe Tomato	1.18003	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.04293	0.877
1-1-2/M82	0.9678	1
12-2/M82	0.79148	0.955
12-4/M82	0.83672	0.272
1-3/M82	0.82882	0.376
2-1-1/M82	0.86487	0.565
2-1/M82	0.85808	0.74
2-6/M82	1.12096	0.505
3-2/M82	1.30013	0.388
4-1-1/M82	1.30441	1
4-1/M82	1.75154	1
4-3-2/M82	2.0025
4-3/M82	0.74706	1
5-3/M82	0.9162	0.642
6-2/M82	1.4122	1
6-3/M82	0.99189	1
7-1/M82	1.5279
7-2/M82	1.57158	0.282
9-3-2/M82	1.82342

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	0.97914	1
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.98749	1
IL12-4/WTpooled	0.98854	1
IL1-4/WTpooled	1.01248	1
WT/WTpooled	1.09895	0.89

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	0.89604	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.06572	0.914
DC3000/delta hrp 6h	0.89766	0.95
DC3000/delta hrp 12h	0.87771	1
DC3000/delta hrp 24h	1.48643	0.041

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.02713	1
DC3000 delta B/DC3000 delta AB	1.13454	0.269

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.01905	1
Exp 36h	0.81722	0.699
Exp 60h	0.84541	0.664

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

hybridization	ratio	FDR (corrected p value)
self-self	1.05445	1
Var 0h	2.33181	0.98
Var 12h I row2-row1	0.88251	0.31
Var 12h NI row2-row1	1.05539	1
Var 36h I row2-row1	1.16301	0.309
Var 36h NI row2-row1	0.96312	0.791
Var 60h I row2-row1	0.8144	0.439
Var 60h NI row2-row1	0.85367	0.359
Time course 0hI-0hNI	1.02885	0.852
Time course 12hI-12hNI	0.96644	0.761
Time course 36hI-36hNI	1.12253	0.039
Time course 60hI-60hNI	1.39908	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)	0.68389	0.237
transgenic ySAMdc/azygous control (breaker)	0.25641	0.132
transgenic ySAMdc/azygous control (red)	1.83716	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.98867	0.694

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.01192	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.76254	0.087
Manapal/WT (break)	1.02377	1
Manapal/WT (red)	1.44738	0.222