Tomato Functional Genomics Database (TFGD)

Expression of 1-1-8.2.7.9

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.45393	0.019
27DAP/17DAP	0.97495	0.992
39DAP/27DAP	0.8968	0.631
41DAP/39DAP	1.25497	0.63
42DAP/41DAP	1.03967	1
43DAP/42DAP	0.83271	0.786
47DAP/43DAP	1.05997	0.746
52DAP/47DAP	0.80651	0.54
57DAP/52DAP	0.74022	0.613

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.09346	0.403
17DAP/reference	0.68181	0.008
27DAP/reference	0.81682	0.141
39DAP/reference	0.84021	0.041
41DAP/reference	0.71445	0.014
42DAP/reference	0.87416	0.046
43DAP/reference	0.97038	0.576
47DAP/reference	0.9028	0.098
52DAP/reference	1.07245	0.32
57DAP/reference	1.22356	0.101

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.71187	0.046
27DAP/17DAP	0.97815	0.887
39DAP/27DAP	1.13965	0.565
41DAP/39DAP	1.03039	0.887
42DAP/41DAP	0.93483	0.584
43DAP/42DAP	0.92043	0.351
47DAP/43DAP	0.94731	0.757
52DAP/47DAP	1.09984	0.713
57DAP/52DAP	1.3993	0.055
57DAP/7DAP	0.84913	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.92474	0.296
17DAP/reference	0.9399	0.22
27DAP/reference	1.00471	1
39DAP/reference	0.96163	0.354
41DAP/reference	1.04231	0.539
42DAP/reference	1.09172	0.686
43DAP/reference	1.07436	0.226
47DAP/reference	1.03437	0.854
52DAP/reference	1.20098	0.015
57DAP/reference	1.15958	0.049

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.87352	0.134
17DAP/reference	0.68513	0.009
27DAP/reference	0.91124	0.188
39DAP/reference	0.84701	0.036
41DAP/reference	1.05949	0.846
42DAP/reference	0.91504	0.055
43DAP/reference	0.76093	0.075
47DAP/reference	0.7787	0.015
52DAP/reference	0.80688	0.016
57DAP/reference	0.60972	0.002

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.88896	0.119
17DAP/reference	0.89189	0.234
27DAP/reference	0.97111	0.539
39DAP/reference	1.08539	0.218
41DAP/reference	1.06188	0.486
42DAP/reference	1.09609	0.194
43DAP/reference	0.97985	0.614
47DAP/reference	0.91968	0.286
52DAP/reference	0.86493	0.204
57DAP/reference	1.34576	0.034

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.97786	1
26DAP/20DAP	0.93427	1
34DAP/26DAP	1.18256	1
51DAP/34DAP	0.72406	0.286
52DAP/51DAP	1.42472	0.163
53DAP/52DAP	0.87726	0.712
55DAP/53DAP	1.50926	0.115
57DAP/55DAP	0.86132	0.375
62DAP/57DAP	1.49454	0.723
68DAP/62DAP	1.21347	0.481
68DAP/14DAP	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.81994	0.102

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.78491	0.236
Mature Green Tomato/Ripe Tomato	0.69646	0.317
Immature Eggplant/Mature Eggplant	2.05659	0.05
Ripe Pepper/Ripe Tomato	0.65085	1
Mature Eggplant/Ripe Tomato	1.01727	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.97666	0.934
1-1-2/M82	1.08426
12-2/M82	1.08616
12-4/M82	1.1069	1
1-3/M82	1.01277
2-1-1/M82	1.19442
2-1/M82	1.21741	1
2-6/M82	1.0551	1
3-2/M82	1.07483
4-1-1/M82	1.03316
4-1/M82	0.98656	1
4-3-2/M82	0.9035	0.698
4-3/M82	1.25062	1
5-3/M82	0.85025
6-2/M82	1.51639
6-3/M82	0.86268
7-1/M82	1.14509
7-2/M82	N/A	N/A
9-3-2/M82	1.21647	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	0.87588
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	0.97162	1
IL1-4/WTpooled	1.15198	1
WT/WTpooled	1.03468	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	0.9902	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.04245	0.921
DC3000/delta hrp 6h	1.13198	1
DC3000/delta hrp 12h	0.86521	1
DC3000/delta hrp 24h	0.90402	0.338

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.98735
DC3000 delta B/DC3000 delta AB	0.81175	0.029

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	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
self-self	1.04435	1
Var 0h	0.48786	1
Var 12h I row2-row1	1.00504	1
Var 12h NI row2-row1	0.91023	0.36
Var 36h I row2-row1	0.95172	0.805
Var 36h NI row2-row1	1.03981	1
Var 60h I row2-row1	1.00962	1
Var 60h NI row2-row1	1.09781	0.904
Time course 0hI-0hNI	0.92117	0.404
Time course 12hI-12hNI	0.88994	0.05
Time course 36hI-36hNI	0.87351	0.211
Time course 60hI-60hNI	0.58533	0.006

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)	0.94855	0.348
transgenic ySAMdc/azygous control (breaker)	0.89646	0.15
transgenic ySAMdc/azygous control (red)	1.06369	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.05008	0.135

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.89389	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.0223	1
Manapal/WT (break)	0.80849	0.333
Manapal/WT (red)	0.88454	0.503