Tomato Functional Genomics Database (TFGD)

Expression of 1-1-4.1.9.20

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.99779	0.83
27DAP/17DAP	1.09112	0.89
39DAP/27DAP	0.68477	0.414
41DAP/39DAP	1.18224	0.814
42DAP/41DAP	0.95695	1
43DAP/42DAP	0.9327	0.874
47DAP/43DAP	1.0971	0.52
52DAP/47DAP	0.92595	0.757
57DAP/52DAP	1.08403	0.969

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.18714	0.097
17DAP/reference	1.24093	0.068
27DAP/reference	1.03102	0.894
39DAP/reference	1.13529	0.037
41DAP/reference	1.23826	0.027
42DAP/reference	0.94534	0.188
43DAP/reference	0.94449	0.302
47DAP/reference	0.96877	0.366
52DAP/reference	0.79835	0.037
57DAP/reference	0.76679	0.017

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.07842	0.899
27DAP/17DAP	1.38663	0.151
39DAP/27DAP	0.74487	0.123
41DAP/39DAP	1.07777	0.853
42DAP/41DAP	1.20337	0.861
43DAP/42DAP	0.86195	0.063
47DAP/43DAP	1.03585	0.934
52DAP/47DAP	1.60544	0.408
57DAP/52DAP	1.05299	0.782
57DAP/7DAP	2.22581

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.89342	0.326
17DAP/reference	1.23426	0.269
27DAP/reference	0.99479	0.656
39DAP/reference	1.32889	0.038
41DAP/reference	1.07141	1
42DAP/reference	1.11896	0.405
43DAP/reference	1.21818	0.105
47DAP/reference	1.04201	0.745
52DAP/reference	1.13254	0.599
57DAP/reference	1.03871	0.966

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.35029	0.038
17DAP/reference	1.12813	0.426
27DAP/reference	0.9434	0.407
39DAP/reference	1.07781	0.67
41DAP/reference	0.76449	0.012
42DAP/reference	0.74252	0.019
43DAP/reference	1.10883	0.268
47DAP/reference	0.82442	0.073
52DAP/reference	1.034	0.629
57DAP/reference	1.14614	0.654

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.95267	0.362
17DAP/reference	1.06577	0.842
27DAP/reference	1.21227	0.032
39DAP/reference	1.06515	0.528
41DAP/reference	1.16861	0.115
42DAP/reference	1.06625	0.907
43DAP/reference	1.10988	0.625
47DAP/reference	0.98023	0.558
52DAP/reference	1.09164	0.639
57DAP/reference	0.74224	0.07

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.06528	0.966
26DAP/20DAP	1.42673
34DAP/26DAP	1.24398	0.819
51DAP/34DAP	1.21755	0.666
52DAP/51DAP	0.75927
53DAP/52DAP	0.97102	0.854
55DAP/53DAP	0.49879	0.042
57DAP/55DAP	0.94103	0.748
62DAP/57DAP	1.35079	0.393
68DAP/62DAP	0.79824	0.227
68DAP/14DAP	0.56797	0.121

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.13242	0.814

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.30426
Immature Eggplant/Mature Eggplant	1.22733	0.05
Ripe Pepper/Ripe Tomato	N/A	N/A
Mature Eggplant/Ripe Tomato	0.88634

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.3216
1-1-2/M82	N/A	N/A
12-2/M82	N/A	N/A
12-4/M82	1.06547	1
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	1.07065
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	1.04711
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	N/A	N/A
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	N/A	N/A
IL1-4/WTpooled	N/A	N/A
WT/WTpooled	N/A	N/A

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	0.81564	0.09

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.02526
DC3000/delta hrp 6h	1.23433
DC3000/delta hrp 12h	1.08459	1
DC3000/delta hrp 24h	0.86107	0.159

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.01445
DC3000 delta B/DC3000 delta AB	N/A	N/A

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	1.04911	1
Var 0h	1.04583	0.936
Var 12h I row2-row1	1.08193
Var 12h NI row2-row1	1.27766	1
Var 36h I row2-row1	1.13151	0.305
Var 36h NI row2-row1	0.60395	1
Var 60h I row2-row1	0.88266	0.285
Var 60h NI row2-row1	1.31512
Time course 0hI-0hNI	0.8002	0.346
Time course 12hI-12hNI	0.97701	0.882
Time course 36hI-36hNI	0.87963	0.088
Time course 60hI-60hNI	0.70661	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)	1.00923	1
transgenic ySAMdc/azygous control (breaker)	1.24165	0.178
transgenic ySAMdc/azygous control (red)	1.064	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.94026	0.067

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.9442	0.268

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.99488	1
Manapal/WT (break)	0.90204	1
Manapal/WT (red)	1.39749	0.134