Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.4.8.8

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.29044	1
27DAP/17DAP	2.02114	0.341
39DAP/27DAP	2.97084	0.099
41DAP/39DAP	2.20742	0.149
42DAP/41DAP	2.99156	0.02
43DAP/42DAP	2.44824	0.661
47DAP/43DAP	0.93893	0.773
52DAP/47DAP	0.45791	0.033
57DAP/52DAP	1.50051	0.908

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.27575	0.024
17DAP/reference	0.29956	0.007
27DAP/reference	0.55177	0.024
39DAP/reference	1.48115	0.786
41DAP/reference	0.87847	0.341
42DAP/reference	3.54171	0.001
43DAP/reference	3.87673	0.006
47DAP/reference	3.05248	0.001
52DAP/reference	1.5471	0.011
57DAP/reference	3.06884	0.011

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.77592	0.164
27DAP/17DAP	0.95992	0.878
39DAP/27DAP	9.01029	0.016
41DAP/39DAP	0.23756	0.013
42DAP/41DAP	4.24363	0.002
43DAP/42DAP	4.65391	0.013
47DAP/43DAP	0.83564	0.243
52DAP/47DAP	1.01322	0.925
57DAP/52DAP	1.1825	0.486
57DAP/7DAP	11.0667	0.204

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.13592	0.042
17DAP/reference	0.135	0.011
27DAP/reference	0.17045	0.01
39DAP/reference	0.63209	0.031
41DAP/reference	0.34656	0.018
42DAP/reference	0.99377	0.393
43DAP/reference	1.86558	0.031
47DAP/reference	2.72127	0.014
52DAP/reference	0.61203	0.02
57DAP/reference	0.60139	0.01

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.15674	0.005
17DAP/reference	0.17418	0.003
27DAP/reference	0.32188	0.008
39DAP/reference	0.27973	0.008
41DAP/reference	0.33156	0.005
42DAP/reference	0.39168	0.01
43DAP/reference	0.26838	0.002
47DAP/reference	0.60691	0.019
52DAP/reference	0.22484	0.003
57DAP/reference	0.32048	0.002

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.11265	0.022
17DAP/reference	0.99388	0.103
27DAP/reference	0.14071	0.02
39DAP/reference	0.2955	0.007
41DAP/reference	0.47962	0.019
42DAP/reference	4.57802	0.006
43DAP/reference	5.83817	0.006
47DAP/reference	3.63689	0.005
52DAP/reference	3.95582	0.028
57DAP/reference	1.65944	0.043

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.14125	0.631
26DAP/20DAP	0.93748	1
34DAP/26DAP	1.20627	0.819
51DAP/34DAP	1.24258	0.654
52DAP/51DAP	1.20707	0.954
53DAP/52DAP	1.06521	1
55DAP/53DAP	1.29915	0.893
57DAP/55DAP	0.88282	0.583
62DAP/57DAP	1.17747	1
68DAP/62DAP	0.89927	0.747
68DAP/14DAP	1.09784	0.578

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	81.2024	0.014

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.11868	0.017
Immature Eggplant/Mature Eggplant	14.7409	0.063
Ripe Pepper/Ripe Tomato	0.13206	0.224
Mature Eggplant/Ripe Tomato	0.0387	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.11418	0.877
1-1-2/M82	1.07622	1
12-2/M82	0.99339	1
12-4/M82	0.98214	0.619
1-3/M82	2.21074	0.255
2-1-1/M82	0.82889	0.465
2-1/M82	1.04925	1
2-6/M82	0.95833	1
3-2/M82	1.1094	0.717
4-1-1/M82	0.89625	1
4-1/M82	0.83092
4-3-2/M82	0.9913	1
4-3/M82	0.87582	0.72
5-3/M82	0.96575	1
6-2/M82	0.98862	1
6-3/M82	1.01054	1
7-1/M82	1.02183	1
7-2/M82	1.01197	1
9-3-2/M82	0.61372	0.355

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	1.28196	0.659
IL7-5/WTpooled	1.21371
IL7-3/WTpooled	1.19987	1
IL12-4/WTpooled	1.24845	0.785
IL1-4/WTpooled	1.5415	1
WT/WTpooled	1.00822	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	1.12025	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.01102	1
DC3000/delta hrp 6h	0.79905	0.95
DC3000/delta hrp 12h	1.09106	1
DC3000/delta hrp 24h	0.50967	0.034

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.90893	0.042
DC3000 delta B/DC3000 delta AB	1.37302	0.097

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	N/A	N/A
Exp 36h	0.90618	0.82
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	N/A	N/A
Var 0h	0.84062	0.933
Var 12h I row2-row1	N/A	N/A
Var 12h NI row2-row1	N/A	N/A
Var 36h I row2-row1	N/A	N/A
Var 36h NI row2-row1	N/A	N/A
Var 60h I row2-row1	N/A	N/A
Var 60h NI row2-row1	N/A	N/A
Time course 0hI-0hNI	N/A	N/A
Time course 12hI-12hNI	N/A	N/A
Time course 36hI-36hNI	N/A	N/A
Time course 60hI-60hNI	N/A	N/A

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)	0.43807	0.246
transgenic ySAMdc/azygous control (breaker)	1.26364	0.248
transgenic ySAMdc/azygous control (red)	1.068	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.63242	0.023

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.3411	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.48746	0.307
Manapal/WT (break)	1.05686	0.381
Manapal/WT (red)	0.76544	0.188