Tomato Functional Genomics Database (TFGD)

Expression of 1-1-4.4.19.8

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.06387	0.904
27DAP/17DAP	1.05387	1
39DAP/27DAP	1.18611	0.823
41DAP/39DAP	1.08193	0.642
42DAP/41DAP	1.2355	0.644
43DAP/42DAP	1.07602	0.94
47DAP/43DAP	0.96205	0.847
52DAP/47DAP	0.75373	0.413
57DAP/52DAP	1.06787	0.98

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.86127	0.14
17DAP/reference	0.91541	0.474
27DAP/reference	0.95489	0.295
39DAP/reference	1.0305	0.8
41DAP/reference	0.90549	0.201
42DAP/reference	1.02182	0.707
43DAP/reference	0.88877	0.594
47DAP/reference	1.30676	0.075
52DAP/reference	1.02169	0.951
57DAP/reference	N/A	N/A

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.2187	0.049
27DAP/17DAP	0.85971	0.195
39DAP/27DAP	1.12686	0.403
41DAP/39DAP	1.03793	1
42DAP/41DAP	1.1034	0.401
43DAP/42DAP	1.79022	0.014
47DAP/43DAP	0.96981	0.861
52DAP/47DAP	1.13145	0.609
57DAP/52DAP	0.9704	0.726
57DAP/7DAP	1.45326	0.365

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.83498	0.168
17DAP/reference	0.75815	0.031
27DAP/reference	0.72385	0.026
39DAP/reference	0.951	0.354
41DAP/reference	0.86607	0.203
42DAP/reference	1.14646	0.534
43DAP/reference	0.90579	0.151
47DAP/reference	0.92725	0.383
52DAP/reference	0.78474	0.057
57DAP/reference	0.77716	0.007

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.02015	0.852
17DAP/reference	1.00537	0.873
27DAP/reference	1.01259	1
39DAP/reference	1.01645	1
41DAP/reference	1.11404	0.439
42DAP/reference	0.90418	0.15
43DAP/reference	0.95432	0.43
47DAP/reference	1.00417	0.812
52DAP/reference	1.01421	0.988
57DAP/reference	1.08258	0.494

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.7841	0.028
17DAP/reference	0.9699	0.624
27DAP/reference	0.85608	0.092
39DAP/reference	0.82336	0.014
41DAP/reference	0.86628	0.167
42DAP/reference	1.2446	0.024
43DAP/reference	1.33182	0.065
47DAP/reference	1.08919	0.239
52DAP/reference	1.39025	0.262
57DAP/reference	1.00848	0.933

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.3292	0.916
26DAP/20DAP	0.98926	1
34DAP/26DAP	1.8068	0.542
51DAP/34DAP	0.97189	0.824
52DAP/51DAP	0.95113	1
53DAP/52DAP	0.63273	0.049
55DAP/53DAP	0.71636	0.021
57DAP/55DAP	1.21828	0.728
62DAP/57DAP	0.96412	0.994
68DAP/62DAP	0.7956	0.406
68DAP/14DAP	0.96423	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.68913	0.021

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.99882	0.805
Mature Green Tomato/Ripe Tomato	0.74757	0.148
Immature Eggplant/Mature Eggplant	0.98364	1
Ripe Pepper/Ripe Tomato	0.24979	0.224
Mature Eggplant/Ripe Tomato	0.45772	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.78009	0.944
1-1-2/M82	1.06159	1
12-2/M82	N/A	N/A
12-4/M82	1.2799	1
1-3/M82	1.78136	0.248
2-1-1/M82	0.93453	0.683
2-1/M82	N/A	N/A
2-6/M82	0.60693
3-2/M82	1.61573	0.717
4-1-1/M82	1.25283	1
4-1/M82	1.23247	0.287
4-3-2/M82	0.8664	0.698
4-3/M82	1.16069	1
5-3/M82	1.03746	1
6-2/M82	0.86436	0.444
6-3/M82	N/A	N/A
7-1/M82	1.3191	0.598
7-2/M82	1.44995
9-3-2/M82	0.91131	0.355

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	1.25192
IL12-4/WTpooled	1.03229	1
IL1-4/WTpooled	0.90902	0.562
WT/WTpooled	0.91082	0.425

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	0.94091	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.07947	0.914
DC3000/delta hrp 6h	1.05824	0.95
DC3000/delta hrp 12h	1.08844	1
DC3000/delta hrp 24h	1.63072	0.033

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.09413	0.183
DC3000 delta B/DC3000 delta AB	1.01012	0.849

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.08128	1
Exp 36h	0.83177	0.426
Exp 60h	0.89983	0.664

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

hybridization	ratio	FDR (corrected p value)
self-self	1.00139	1
Var 0h	N/A	N/A
Var 12h I row2-row1	0.95919	0.627
Var 12h NI row2-row1	1.10302	0.649
Var 36h I row2-row1	1.26242	0.489
Var 36h NI row2-row1	0.88018	0.645
Var 60h I row2-row1	1.11374	1
Var 60h NI row2-row1	0.92652	0.69
Time course 0hI-0hNI	1.07014	0.603
Time course 12hI-12hNI	0.99394	1
Time course 36hI-36hNI	0.97954	0.549
Time course 60hI-60hNI	0.86671	0.011

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)	0.90894	0.314
transgenic ySAMdc/azygous control (breaker)	0.83747	0.15
transgenic ySAMdc/azygous control (red)	0.96636	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.94506	0.117

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.36268	0.229

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	N/A	N/A
Manapal/WT (break)	1.05699	1
Manapal/WT (red)	1.33858	0.222