Tomato Functional Genomics Database (TFGD)

Expression of 1-1-8.2.12.18

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.88892	0.445
27DAP/17DAP	0.88064	0.717
39DAP/27DAP	0.81504	0.421
41DAP/39DAP	1.07293	0.797
42DAP/41DAP	0.67738	0.397
43DAP/42DAP	1.04042	0.937
47DAP/43DAP	0.95951	0.754
52DAP/47DAP	1.31444	0.718
57DAP/52DAP	1.1839	0.964

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.98376	0.707
17DAP/reference	1.17167	0.096
27DAP/reference	1.24811	0.05
39DAP/reference	1.04234	0.8
41DAP/reference	1.27955	0.221
42DAP/reference	1.17314	0.383
43DAP/reference	0.96373	0.653
47DAP/reference	1.11971	0.478
52DAP/reference	0.97024	0.489
57DAP/reference	0.93929	0.248

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.63014	0.027
27DAP/17DAP	1.1374	0.518
39DAP/27DAP	0.80773	0.198
41DAP/39DAP	0.79071	0.276
42DAP/41DAP	1.04959	1
43DAP/42DAP	0.96257	0.774
47DAP/43DAP	0.84822	0.214
52DAP/47DAP	0.91369	0.753
57DAP/52DAP	0.92628	0.581
57DAP/7DAP	0.57021	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.02577	0.894
17DAP/reference	0.99213	0.599
27DAP/reference	1.00842	1
39DAP/reference	0.82694	0.095
41DAP/reference	0.90008	0.16
42DAP/reference	0.96653	0.458
43DAP/reference	0.88945	0.105
47DAP/reference	0.80333	0.066
52DAP/reference	1.04483	0.428
57DAP/reference	0.95813	0.382

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.45556	0.17
17DAP/reference	1.316	0.017
27DAP/reference	1.35609	0.225
39DAP/reference	0.91956	0.265
41DAP/reference	1.05788	0.72
42DAP/reference	N/A	N/A
43DAP/reference	1.62508	0.052
47DAP/reference	1.07025
52DAP/reference	1.25388	0.036
57DAP/reference	1.39166	0.028

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.94058	0.311
17DAP/reference	1.07733	0.585
27DAP/reference	1.05944	0.644
39DAP/reference	1.06163	0.67
41DAP/reference	0.96456	0.512
42DAP/reference	1.14503	0.108
43DAP/reference	0.84016	0.137
47DAP/reference	1.06173	0.76
52DAP/reference	0.91847	0.36
57DAP/reference	0.85758	0.234

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.27784	0.966
26DAP/20DAP	0.53999	0.317
34DAP/26DAP	1.23097	0.819
51DAP/34DAP	1.04114	0.901
52DAP/51DAP	1.11338	0.808
53DAP/52DAP	0.74838	0.288
55DAP/53DAP	1.06893	0.955
57DAP/55DAP	1.19439	0.626
62DAP/57DAP	1.24618	0.445
68DAP/62DAP	0.86258	0.464
68DAP/14DAP	0.67148	0.121

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.0018	0.696

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	3.82555	0.058
Mature Green Tomato/Ripe Tomato	1.78611	0.018
Immature Eggplant/Mature Eggplant	0.52839	0.062
Ripe Pepper/Ripe Tomato	2.50696	1
Mature Eggplant/Ripe Tomato	23.3199	0.373

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.98551	0.961
1-1-2/M82	1.41068
12-2/M82	1.14569	1
12-4/M82	1.12994	1
1-3/M82	N/A	N/A
2-1-1/M82	0.88532	0.683
2-1/M82	N/A	N/A
2-6/M82	0.84803	0.501
3-2/M82	0.84355
4-1-1/M82	0.80867	1
4-1/M82	0.82174
4-3-2/M82	0.83191	0.487
4-3/M82	1.03085	1
5-3/M82	0.94194	0.387
6-2/M82	N/A	N/A
6-3/M82	1.10469
7-1/M82	0.93867
7-2/M82	0.86569
9-3-2/M82	0.7588	0.355

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.05953	1
IL2-6/WTpooled	1.16467	0.584
IL7-5/WTpooled	0.71953	1
IL7-3/WTpooled	1.12843	1
IL12-4/WTpooled	0.99064	1
IL1-4/WTpooled	1.00193	1
WT/WTpooled	1.01779	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	0.85742	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.08302	0.846
DC3000/delta hrp 6h	1.0216	1
DC3000/delta hrp 12h	1.05702	1
DC3000/delta hrp 24h	0.80302	0.126

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.30243	0.023
DC3000 delta B/DC3000 delta AB	0.48765	0.02

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.94353	1
Exp 36h	0.63449	0.456
Exp 60h	0.64434	0.343

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

hybridization	ratio	FDR (corrected p value)
self-self	1.01215	1
Var 0h	0.3425	1
Var 12h I row2-row1	0.90676	0.338
Var 12h NI row2-row1	0.87895	0.488
Var 36h I row2-row1	0.83721	0.34
Var 36h NI row2-row1	1.25193	1
Var 60h I row2-row1	1.13793	0.562
Var 60h NI row2-row1	1.11433	0.904
Time course 0hI-0hNI	1.02744	0.852
Time course 12hI-12hNI	0.90471	0.393
Time course 36hI-36hNI	0.67857	0.023
Time course 60hI-60hNI	0.17925	0.005

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)	0.84579	0.391
transgenic ySAMdc/azygous control (breaker)	1.26345	0.248
transgenic ySAMdc/azygous control (red)	1.15847	0.92

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	4.47812	0.227

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	2.24351	0.088
Manapal/WT (break)	1.81115	1
Manapal/WT (red)	1.61402	0.142