Tomato Functional Genomics Database (TFGD)

Expression of 1-1-6.4.13.4

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.11275	0.838
27DAP/17DAP	1.16207	0.845
39DAP/27DAP	1.31163	0.566
41DAP/39DAP	1.28586	0.597
42DAP/41DAP	1.18613	0.903
43DAP/42DAP	1.06806	1
47DAP/43DAP	1.11266	0.668
52DAP/47DAP	0.941	0.698
57DAP/52DAP	1.33533	0.969

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.98118	0.578
17DAP/reference	1.13164	0.201
27DAP/reference	1.05451	0.487
39DAP/reference	0.97859	0.762
41DAP/reference	0.95968	0.341
42DAP/reference	1.06844	0.144
43DAP/reference	0.96529	0.631
47DAP/reference	1.0111	0.937
52DAP/reference	0.93663	0.319
57DAP/reference	0.94812	0.415

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.15727	0.749
27DAP/17DAP	0.83918	0.614
39DAP/27DAP	1.06396	1
41DAP/39DAP	1.44913	0.612
42DAP/41DAP	1.12006	0.893
43DAP/42DAP	0.86795	0.336
47DAP/43DAP	0.9841	0.923
52DAP/47DAP	1.02446	0.97
57DAP/52DAP	0.88109	0.348
57DAP/7DAP	0.78316	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.38283	0.085
17DAP/reference	0.98484	0.518
27DAP/reference	1.12768	0.301
39DAP/reference	1.46405	0.007
41DAP/reference	1.22141	0.336
42DAP/reference	1.54152	0.012
43DAP/reference	2.58448	0.006
47DAP/reference	2.25223	0.016
52DAP/reference	1.67798	0.007
57DAP/reference	1.67091	0.004

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.86982	0.083
17DAP/reference	0.79352	0.004
27DAP/reference	0.96426	0.452
39DAP/reference	1.11547	0.477
41DAP/reference	0.96953	0.393
42DAP/reference	1.14639	0.162
43DAP/reference	0.77073	0.048
47DAP/reference	1.09088	0.052
52DAP/reference	0.86368	0.037
57DAP/reference	0.82791	0.058

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.10636	0.347
17DAP/reference	0.76155	0.136
27DAP/reference	1.36566	0.021
39DAP/reference	1.65503	0.016
41DAP/reference	1.2332	0.077
42DAP/reference	1.33118	0.07
43DAP/reference	1.54961	0.041
47DAP/reference	1.01553	1
52DAP/reference	1.80475	0.055
57DAP/reference	2.04024	0.011

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.97166	1
26DAP/20DAP	2.578	0.962
34DAP/26DAP	2.6537	0.819
51DAP/34DAP	1.3097	0.84
52DAP/51DAP	1.74314	0.041
53DAP/52DAP	1.22768	0.043
55DAP/53DAP	1.16019	0.095
57DAP/55DAP	0.37111	0.017
62DAP/57DAP	1.11454	0.935
68DAP/62DAP	7.70131	0.026
68DAP/14DAP	6.41444	0.019

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.38302	0.024

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.87881	0.377
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	0.89002
Mature Eggplant/Ripe Tomato	0.7523

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.92391	0.944
1-1-2/M82	0.89843	0.958
12-2/M82	0.96538	0.955
12-4/M82	1.27595	1
1-3/M82	0.69455
2-1-1/M82	1.16651
2-1/M82	N/A	N/A
2-6/M82	1.15156	0.505
3-2/M82	0.90635	1
4-1-1/M82	0.94136	1
4-1/M82	1.09694	1
4-3-2/M82	0.89011	0.698
4-3/M82	0.75601	1
5-3/M82	0.97121	1
6-2/M82	0.86112	1
6-3/M82	0.54129
7-1/M82	0.75465
7-2/M82	1.15008	1
9-3-2/M82	1.12576	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	0.83717	0.473
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.95917	1
IL12-4/WTpooled	1.00039	1
IL1-4/WTpooled	1.14494
WT/WTpooled	1.01826	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	0.99451	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.8784	0.664
DC3000/delta hrp 6h	1.60003	0.582
DC3000/delta hrp 12h	1.20345	1
DC3000/delta hrp 24h	1.08501	0.453

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.40849	0.043
DC3000 delta B/DC3000 delta AB	1.31837	0.133

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.31714	1
Exp 36h	2.21669	0.693
Exp 60h	1.34741	1

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

hybridization	ratio	FDR (corrected p value)
self-self	0.99528	1
Var 0h	0.49729	1
Var 12h I row2-row1	1.45038	0.176
Var 12h NI row2-row1	1.38647	0.281
Var 36h I row2-row1	0.8447	1
Var 36h NI row2-row1	2.83059	0.276
Var 60h I row2-row1	0.31884	0.285
Var 60h NI row2-row1	0.97455	1
Time course 0hI-0hNI	0.77268	0.163
Time course 12hI-12hNI	1.16072	0.639
Time course 36hI-36hNI	0.88558	0.269
Time course 60hI-60hNI	2.37317	0.009

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)	2.05217	0.3
transgenic ySAMdc/azygous control (breaker)	0.64061	0.251
transgenic ySAMdc/azygous control (red)	2.58043	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.58985	0.027

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.46702	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.17243	0.105
Manapal/WT (break)	9.30753	0.381
Manapal/WT (red)	2.42946	0.222