Tomato Functional Genomics Database (TFGD)

Expression of 1-1-4.4.14.8

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.00406	0.76
27DAP/17DAP	0.96559	0.934
39DAP/27DAP	0.91804	0.641
41DAP/39DAP	1.24404	0.545
42DAP/41DAP	1.01111	1
43DAP/42DAP	1.00966	0.937
47DAP/43DAP	1.38134	0.842
52DAP/47DAP	1.47116	0.346
57DAP/52DAP	0.98932	0.926

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.89688	0.149
17DAP/reference	0.8073	0.018
27DAP/reference	1.02684	1
39DAP/reference	0.78753	0.012
41DAP/reference	0.77851	0.039
42DAP/reference	0.69703	0.001
43DAP/reference	0.89759	0.045
47DAP/reference	0.88974	0.106
52DAP/reference	0.89513	0.275
57DAP/reference	1.13255	0.079

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.9294	0.428
27DAP/17DAP	0.87054	0.143
39DAP/27DAP	0.80461	0.45
41DAP/39DAP	1.40662	0.469
42DAP/41DAP	0.77709	0.054
43DAP/42DAP	0.82013	0.189
47DAP/43DAP	1.21846	0.884
52DAP/47DAP	0.87426	0.719
57DAP/52DAP	1.29953	0.594
57DAP/7DAP	1.16199	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.44908	0.045
17DAP/reference	1.90907	0.006
27DAP/reference	1.82253	0.006
39DAP/reference	1.90952	0.008
41DAP/reference	1.96898	0.011
42DAP/reference	2.00537	0.009
43DAP/reference	2.72094	0.007
47DAP/reference	1.41278	0.219
52DAP/reference	2.06762	0.007
57DAP/reference	1.82838	0.023

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.87075	0.096
17DAP/reference	0.83436	0.083
27DAP/reference	0.83861	0.039
39DAP/reference	0.96488	0.404
41DAP/reference	0.80007	0.08
42DAP/reference	0.97101	0.482
43DAP/reference	0.75674	0.054
47DAP/reference	0.837	0.02
52DAP/reference	0.91766	0.101
57DAP/reference	0.88202	0.125

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.66073	0.036
17DAP/reference	1.38473	0.398
27DAP/reference	2.06314	0.021
39DAP/reference	1.87671	0.013
41DAP/reference	1.54719	0.015
42DAP/reference	1.71127	0.01
43DAP/reference	1.54748	0.073
47DAP/reference	0.93544	0.269
52DAP/reference	1.55141	0.268
57DAP/reference	1.619	0.175

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.45589	0.878
26DAP/20DAP	0.86796	1
34DAP/26DAP	0.77868	0.488
51DAP/34DAP	0.79943	0.127
52DAP/51DAP	1.14043	0.776
53DAP/52DAP	1.05545	0.97
55DAP/53DAP	0.99319	0.864
57DAP/55DAP	0.9938	0.935
62DAP/57DAP	0.92932	0.871
68DAP/62DAP	1.2171	0.878
68DAP/14DAP	1.62182	0.021

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.9294	0.422

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.63011
Mature Green Tomato/Ripe Tomato	N/A	N/A
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	N/A	N/A
Mature Eggplant/Ripe Tomato	N/A	N/A

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	N/A	N/A
12-2/M82	N/A	N/A
12-4/M82	N/A	N/A
1-3/M82	N/A	N/A
2-1-1/M82	N/A	N/A
2-1/M82	N/A	N/A
2-6/M82	N/A	N/A
3-2/M82	N/A	N/A
4-1-1/M82	N/A	N/A
4-1/M82	N/A	N/A
4-3-2/M82	N/A	N/A
4-3/M82	N/A	N/A
5-3/M82	N/A	N/A
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	N/A	N/A
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.01311	1
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	1.34653	0.792
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	1.12866	0.839
IL1-4/WTpooled	0.96123	1
WT/WTpooled	0.99866	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	0.80419	0.75

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.9793	1
DC3000/delta hrp 6h	1.00935	1
DC3000/delta hrp 12h	0.9056	1
DC3000/delta hrp 24h	0.38856	0.034

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.3719	0.023
DC3000 delta B/DC3000 delta AB	0.45244	0.025

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.75393	1
Exp 36h	0.72022	0.539
Exp 60h	0.46492	0.253

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

hybridization	ratio	FDR (corrected p value)
self-self	1.02583	1
Var 0h	0.86353	0.933
Var 12h I row2-row1	0.85006	0.565
Var 12h NI row2-row1	1.08804	1
Var 36h I row2-row1	0.88561	0.313
Var 36h NI row2-row1	1.39455	0.253
Var 60h I row2-row1	1.15596
Var 60h NI row2-row1	1.2152	0.904
Time course 0hI-0hNI	1.03839	0.852
Time course 12hI-12hNI	1.03726	0.714
Time course 36hI-36hNI	0.81776	0.023
Time course 60hI-60hNI	0.10098	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)	0.84583	0.377
transgenic ySAMdc/azygous control (breaker)	1.45778	0.178
transgenic ySAMdc/azygous control (red)	1.60882	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.9638	0.248

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.58459	0.233

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	5.17591	0.083
Manapal/WT (break)	2.88755	0.123
Manapal/WT (red)	1.77479	0.126