Tomato Functional Genomics Database (TFGD)

Expression of 1-1-5.3.7.7

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.98048	0.83
27DAP/17DAP	0.93191	0.863
39DAP/27DAP	0.9953	0.798
41DAP/39DAP	0.97679	0.893
42DAP/41DAP	1.04	0.978
43DAP/42DAP	0.99862	0.937
47DAP/43DAP	1.01582	0.979
52DAP/47DAP	0.97731	0.906
57DAP/52DAP	1.07481	0.935

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.00322	0.787
17DAP/reference	0.93883	0.028
27DAP/reference	0.90611	0.215
39DAP/reference	0.95553	0.391
41DAP/reference	0.88581	0.201
42DAP/reference	0.98826	0.469
43DAP/reference	1.00054	1
47DAP/reference	0.91435	0.003
52DAP/reference	0.90943	0.108
57DAP/reference	0.89459	0.047

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.08041	0.271
27DAP/17DAP	0.93957	0.684
39DAP/27DAP	0.91813	0.218
41DAP/39DAP	1.06929	0.623
42DAP/41DAP	1.08859	0.687
43DAP/42DAP	0.96516	0.597
47DAP/43DAP	0.93534	0.447
52DAP/47DAP	1.14586	0.666
57DAP/52DAP	1.19193	0.193
57DAP/7DAP	0.71082	0.181

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.06754	0.435
17DAP/reference	0.98956	0.518
27DAP/reference	0.99266	0.656
39DAP/reference	0.94313	0.039
41DAP/reference	1.0461	0.475
42DAP/reference	1.0442	0.534
43DAP/reference	0.98394	0.48
47DAP/reference	1.01605	0.868
52DAP/reference	1.12192	0.081
57DAP/reference	1.08905	0.043

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.03886	0.695
17DAP/reference	1.08397	0.113
27DAP/reference	1.07065	0.769
39DAP/reference	1.03073	0.935
41DAP/reference	1.10814	0.427
42DAP/reference	1.0467	1
43DAP/reference	1.01612	0.89
47DAP/reference	0.9212	0.032
52DAP/reference	0.93901	0.121
57DAP/reference	0.90691	0.079

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.98677
17DAP/reference	1.03606	0.627
27DAP/reference	N/A	N/A
39DAP/reference	0.96737	0.328
41DAP/reference	0.93314	0.119
42DAP/reference	0.99063	0.816
43DAP/reference	0.95763	0.281
47DAP/reference	0.96473	0.325
52DAP/reference	0.93693	0.505
57DAP/reference	0.92772	0.174

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.95017	1
26DAP/20DAP	1.19141	0.826
34DAP/26DAP	1.32127	1
51DAP/34DAP	1.00172	0.883
52DAP/51DAP	1.99795	0.037
53DAP/52DAP	0.85784
55DAP/53DAP	1.05155	0.861
57DAP/55DAP	0.79947	0.281
62DAP/57DAP	1.15992	0.678
68DAP/62DAP	0.97885	0.834
68DAP/14DAP	1.03866	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.57667	0.031

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.09368	0.176
Mature Green Tomato/Ripe Tomato	0.92837	0.522
Immature Eggplant/Mature Eggplant	1.29081	0.054
Ripe Pepper/Ripe Tomato	1.9774	1
Mature Eggplant/Ripe Tomato	1.2032	0.373

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.05544	0.877
1-1-2/M82	1.33983
12-2/M82	0.82786
12-4/M82	1.05442	1
1-3/M82	1.04335	1
2-1-1/M82	1.10369
2-1/M82	0.4201
2-6/M82	0.90039	0.501
3-2/M82	0.99759
4-1-1/M82	0.92397	1
4-1/M82	1.12012	0.512
4-3-2/M82	1.0481	1
4-3/M82	1.04116	1
5-3/M82	1.0979	1
6-2/M82	0.90353
6-3/M82	0.84241	1
7-1/M82	N/A	N/A
7-2/M82	1.039	1
9-3-2/M82	1.04936	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	1.02991	1
IL7-5/WTpooled	1.51906
IL7-3/WTpooled	1.1655	1
IL12-4/WTpooled	1.14007	0.695
IL1-4/WTpooled	1.12899	1
WT/WTpooled	1.01748	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	0.97136	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.04083	0.921
DC3000/delta hrp 6h	1.0315	1
DC3000/delta hrp 12h	0.89233	1
DC3000/delta hrp 24h	0.88709	0.285

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.11087	0.16
DC3000 delta B/DC3000 delta AB	1.21434	0.226

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.89512	1
Exp 36h	0.91389	0.879
Exp 60h	0.9428	0.855

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

hybridization	ratio	FDR (corrected p value)
self-self	0.98129	1
Var 0h	1.09863	0.936
Var 12h I row2-row1	0.87507	0.338
Var 12h NI row2-row1	0.97985	0.906
Var 36h I row2-row1	1.09624	0.908
Var 36h NI row2-row1	1.13636	1
Var 60h I row2-row1	0.96099	0.582
Var 60h NI row2-row1	1.02157	1
Time course 0hI-0hNI	0.89749	0.247
Time course 12hI-12hNI	1.02532	0.818
Time course 36hI-36hNI	0.97344	0.533
Time course 60hI-60hNI	0.84617	0.026

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)	0.92195	0.286
transgenic ySAMdc/azygous control (breaker)	1.54982	0.166
transgenic ySAMdc/azygous control (red)	1.07647	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.0291	0.135

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.7345	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.88128	1
Manapal/WT (break)	1.08135	0.14
Manapal/WT (red)	1.99803	0.222