Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.2.1.16

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.59405	0.015
27DAP/17DAP	0.91168	0.777
39DAP/27DAP	0.76272	0.414
41DAP/39DAP	1.11893	0.96
42DAP/41DAP	1.0836	0.933
43DAP/42DAP	1.06864	1
47DAP/43DAP	0.93754	0.705
52DAP/47DAP	1.14601	0.95
57DAP/52DAP	0.99909	0.983

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.87051	0.121
17DAP/reference	0.89991	0.278
27DAP/reference	0.86913	0.089
39DAP/reference	0.92212	0.333
41DAP/reference	0.85645	0.026
42DAP/reference	0.94882	0.088
43DAP/reference	0.95272	0.394
47DAP/reference	0.88067	0.021
52DAP/reference	0.86619	0.051
57DAP/reference	0.87929	0.047

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.86389	0.388
27DAP/17DAP	0.83624	0.195
39DAP/27DAP	0.77289	0.251
41DAP/39DAP	0.95393	0.849
42DAP/41DAP	0.87802	0.439
43DAP/42DAP	0.9706	0.774
47DAP/43DAP	0.95724	0.833
52DAP/47DAP	1.21995	0.428
57DAP/52DAP	1.43557	0.145
57DAP/7DAP	2.18617	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.94171	0.203
17DAP/reference	1.04441	1
27DAP/reference	1.2489	0.01
39DAP/reference	1.06538	0.96
41DAP/reference	1.25129	0.08
42DAP/reference	1.16343	0.534
43DAP/reference	0.8693	0.044
47DAP/reference	1.08135	0.44
52DAP/reference	0.98529	0.571
57DAP/reference	1.21422	0.087

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.80556	0.028
17DAP/reference	0.65467	0.005
27DAP/reference	0.74431	0.018
39DAP/reference	0.84736	0.012
41DAP/reference	0.8984	0.07
42DAP/reference	0.88556	0.046
43DAP/reference	0.93452	0.459
47DAP/reference	0.95666	0.129
52DAP/reference	0.86979	0.047
57DAP/reference	0.73281	0.046

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.19793	0.081
17DAP/reference	1.33925	0.243
27DAP/reference	1.132	0.062
39DAP/reference	1.32921	0.157
41DAP/reference	1.17235	0.086
42DAP/reference	1.07667	0.5
43DAP/reference	1.03114	0.867
47DAP/reference	1.01062	1
52DAP/reference	1.04935	0.941
57DAP/reference	1.01504	0.92

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.23715	0.85
26DAP/20DAP	1.42622	0.141
34DAP/26DAP	0.98476	1
51DAP/34DAP	1.04862	0.854
52DAP/51DAP	0.86283	1
53DAP/52DAP	0.9265	0.767
55DAP/53DAP	0.75357	0.282
57DAP/55DAP	1.08456	0.927
62DAP/57DAP	1.01581	1
68DAP/62DAP	0.83406	0.406
68DAP/14DAP	1.4578	0.419

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.73466	0.175

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.72833	0.089
Mature Green Tomato/Ripe Tomato	2.4907	0.053
Immature Eggplant/Mature Eggplant	0.45871	0.062
Ripe Pepper/Ripe Tomato	1.83547	1
Mature Eggplant/Ripe Tomato	3.25425

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.94039	0.944
1-1-2/M82	1.03617	1
12-2/M82	1.0768
12-4/M82	0.80609
1-3/M82	0.9117	1
2-1-1/M82	0.87516	0.465
2-1/M82	N/A	N/A
2-6/M82	0.9604	1
3-2/M82	0.58972
4-1-1/M82	1.04634
4-1/M82	1.17901
4-3-2/M82	N/A	N/A
4-3/M82	N/A	N/A
5-3/M82	1.00859	1
6-2/M82	0.89829
6-3/M82	1.03289
7-1/M82	N/A	N/A
7-2/M82	0.68992	0.57
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.68332	0.247
IL2-6/WTpooled	0.74951	0.473
IL7-5/WTpooled	0.79946
IL7-3/WTpooled	0.85381	1
IL12-4/WTpooled	1.02496	1
IL1-4/WTpooled	1.04654	1
WT/WTpooled	0.92126	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	0.8007	0.226

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.06101	0.921
DC3000/delta hrp 6h	1.20012	1
DC3000/delta hrp 12h	1.30628	1
DC3000/delta hrp 24h	0.88611	0.19

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.77396	0.436
DC3000 delta B/DC3000 delta AB	0.55176	0.02

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.13186	1
Exp 36h	1.16577	1
Exp 60h	1.35019	0.399

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

hybridization	ratio	FDR (corrected p value)
self-self	0.96682	1
Var 0h	0.86305	0.374
Var 12h I row2-row1	0.77326	0.353
Var 12h NI row2-row1	1.0905	1
Var 36h I row2-row1	0.9911	1
Var 36h NI row2-row1	1.17687	1
Var 60h I row2-row1	1.10823	1
Var 60h NI row2-row1	0.83869	0.301
Time course 0hI-0hNI	0.96512	0.821
Time course 12hI-12hNI	0.96323	0.701
Time course 36hI-36hNI	0.77689	0.056
Time course 60hI-60hNI	0.09872	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)	1.1238	0.339
transgenic ySAMdc/azygous control (breaker)	2.84602	0.166
transgenic ySAMdc/azygous control (red)	1.41055	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.00197	1

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.96329	0.59

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	3.3234	0.083
Manapal/WT (break)	2.32733	0.183
Manapal/WT (red)	2.07267	0.126