Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.1.11.7

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.12051	0.863
27DAP/17DAP	1.31813	0.749
39DAP/27DAP	1.1047	0.876
41DAP/39DAP	1.34823	0.408
42DAP/41DAP	1.04446	1
43DAP/42DAP	1.12996	1
47DAP/43DAP	0.89616	0.652
52DAP/47DAP	1.20507	0.763
57DAP/52DAP	1.00577	0.988

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.82862	0.371
17DAP/reference	1.13753	0.061
27DAP/reference	N/A	N/A
39DAP/reference	N/A	N/A
41DAP/reference	0.97264	0.814
42DAP/reference	1.22646	0.504
43DAP/reference	N/A	N/A
47DAP/reference	1.03503	1
52DAP/reference	0.97169	0.275
57DAP/reference	N/A	N/A

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.99271	0.826
27DAP/17DAP	1.00859	1
39DAP/27DAP	1.00029	1
41DAP/39DAP	1.00561	1
42DAP/41DAP	1.01622	1
43DAP/42DAP	1.05273	0.446
47DAP/43DAP	1.00997	0.969
52DAP/47DAP	0.9995	0.962
57DAP/52DAP	1.00197	0.905
57DAP/7DAP	1.32028	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.88493	0.077
17DAP/reference	0.98026	0.389
27DAP/reference	0.87198	0.01
39DAP/reference	0.95241	0.049
41DAP/reference	0.96397	0.311
42DAP/reference	0.97609	0.178
43DAP/reference	0.95203	0.132
47DAP/reference	0.84761	0.05
52DAP/reference	0.92052	0.049
57DAP/reference	0.94387	0.057

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.10547	0.241
17DAP/reference	1.00062	0.786
27DAP/reference	0.88332	0.139
39DAP/reference	0.91043	0.144
41DAP/reference	0.96644	0.451
42DAP/reference	0.96073	0.433
43DAP/reference	1.03991	0.986
47DAP/reference	0.98992	0.643
52DAP/reference	0.92822	0.143
57DAP/reference	1.07361	0.462

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.94193	0.183
17DAP/reference	1.07641	0.728
27DAP/reference	0.91617	0.067
39DAP/reference	0.91907	0.022
41DAP/reference	0.94648	0.331
42DAP/reference	0.81491	0.071
43DAP/reference	0.84098	0.171
47DAP/reference	0.89586	0.231
52DAP/reference	0.89619	0.262
57DAP/reference	0.68571	0.016

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.00823	0.966
26DAP/20DAP	0.90418	0.512
34DAP/26DAP	0.91532	0.548
51DAP/34DAP	0.87591	0.268
52DAP/51DAP	1.02376	0.821
53DAP/52DAP	0.9791	0.891
55DAP/53DAP	0.86348	0.016
57DAP/55DAP	1.07223	0.968
62DAP/57DAP	1.12085	1
68DAP/62DAP	1.02637	0.939
68DAP/14DAP	0.93675	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.94801	0.422

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.93396	0.446
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	1.89045
Mature Eggplant/Ripe Tomato	1.92616	0.373

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.99677	1
1-1-2/M82	1.02052	1
12-2/M82	1.05772	1
12-4/M82	1.04629	1
1-3/M82	0.84861	0.378
2-1-1/M82	1.10401	0.764
2-1/M82	1.22327	1
2-6/M82	1.12335	0.695
3-2/M82	0.93629	1
4-1-1/M82	1.0702	1
4-1/M82	0.96316	1
4-3-2/M82	0.76828	0.487
4-3/M82	0.79827	0.578
5-3/M82	0.94998	1
6-2/M82	0.87882	1
6-3/M82	1.01715	1
7-1/M82	N/A	N/A
7-2/M82	0.99143	1
9-3-2/M82	0.85003	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.46438	0.277
IL2-6/WTpooled	0.65577	0.473
IL7-5/WTpooled	0.80014	1
IL7-3/WTpooled	1.84469	0.362
IL12-4/WTpooled	1.15522	0.839
IL1-4/WTpooled	1.3887	0.426
WT/WTpooled	1.01858	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	1.04207	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.04656	0.875
DC3000/delta hrp 6h	N/A	N/A
DC3000/delta hrp 12h	0.98262	1
DC3000/delta hrp 24h	1.02984	0.76

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.22076	0.047
DC3000 delta B/DC3000 delta AB	1.01657	0.748

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	N/A	N/A
Exp 36h	N/A	N/A
Exp 60h	1.56076	0.22

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

hybridization	ratio	FDR (corrected p value)
self-self	1.02024	1
Var 0h	0.81012	0.933
Var 12h I row2-row1	1.29336	0.296
Var 12h NI row2-row1	0.82203	0.494
Var 36h I row2-row1	0.81756	0.805
Var 36h NI row2-row1	0.98801	0.743
Var 60h I row2-row1	1.56387	0.562
Var 60h NI row2-row1	1.25939	0.904
Time course 0hI-0hNI	1.09234	0.833
Time course 12hI-12hNI	1.03492	0.786
Time course 36hI-36hNI	0.97172	0.484
Time course 60hI-60hNI	1.21739	0.042

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)	1.06036	0.612
transgenic ySAMdc/azygous control (breaker)	1.11272	1
transgenic ySAMdc/azygous control (red)	0.95366	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.01707	0.448

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.12846	1
Manapal/WT (break)	1.01433	1
Manapal/WT (red)	0.81011	0.229