Tomato Functional Genomics Database (TFGD)

Expression of 1-1-6.4.11.17

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.04745	0.932
27DAP/17DAP	1.055	1
39DAP/27DAP	0.82022	0.462
41DAP/39DAP	1.79269	0.225
42DAP/41DAP	1.02562	1
43DAP/42DAP	0.85656	0.765
47DAP/43DAP	1.24332	0.576
52DAP/47DAP	1.74331	0.205
57DAP/52DAP	0.94417	0.926

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.95724	0.269
17DAP/reference	1.07474	0.083
27DAP/reference	1.0597	0.457
39DAP/reference	1.17379	0.218
41DAP/reference	1.17291	0.023
42DAP/reference	0.92889	0.045
43DAP/reference	1.03325	0.758
47DAP/reference	0.9119	0.012
52DAP/reference	0.92796	0.275
57DAP/reference	0.76591	0.031

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.95981	0.644
27DAP/17DAP	1.12667	0.537
39DAP/27DAP	1.08857	0.347
41DAP/39DAP	1.06086	1
42DAP/41DAP	1.05166	1
43DAP/42DAP	1.05831	0.788
47DAP/43DAP	0.99855	0.977
52DAP/47DAP	1.00883	0.962
57DAP/52DAP	0.84254	0.501
57DAP/7DAP	1.54102	0.365

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.84532	0.071
17DAP/reference	0.87622	0.011
27DAP/reference	0.84143	0.01
39DAP/reference	0.90022	0.021
41DAP/reference	0.89549	0.024
42DAP/reference	0.82281	0.011
43DAP/reference	0.76735	0.023
47DAP/reference	0.76423	0.044
52DAP/reference	0.73482	0.012
57DAP/reference	0.77914	0.009

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.98988	0.831
17DAP/reference	0.97412	0.447
27DAP/reference	0.90619	0.352
39DAP/reference	0.85288	0.152
41DAP/reference	0.78659	0.071
42DAP/reference	0.89925	0.212
43DAP/reference	1.10197	0.338
47DAP/reference	0.96835	0.4
52DAP/reference	0.9979	0.713
57DAP/reference	1.1719	0.236

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.88836	0.127
17DAP/reference	0.99057	0.751
27DAP/reference	0.86514	0.025
39DAP/reference	0.90113	0.092
41DAP/reference	0.89276	0.05
42DAP/reference	0.7685	0.017
43DAP/reference	0.72045	0.076
47DAP/reference	0.9585	0.452
52DAP/reference	0.98999	0.781
57DAP/reference	0.41834	0.018

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.0796	0.966
26DAP/20DAP	0.9456	1
34DAP/26DAP	1.17675	0.819
51DAP/34DAP	0.80515	0.078
52DAP/51DAP	1.08803	0.638
53DAP/52DAP	1.02146	1
55DAP/53DAP	1.28397	0.074
57DAP/55DAP	1.19214	0.51
62DAP/57DAP	1.0768	0.569
68DAP/62DAP	0.83099	0.29
68DAP/14DAP	0.91357	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.7174	0.083

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	1.00716	0.898
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	1.01606	1
1-1-2/M82	0.8129	0.804
12-2/M82	1.13515	1
12-4/M82	0.9423	1
1-3/M82	0.86545	0.378
2-1-1/M82	0.97188	0.784
2-1/M82	N/A	N/A
2-6/M82	1.05714	0.594
3-2/M82	0.98444	1
4-1-1/M82	0.84228	0.962
4-1/M82	1.23818	0.512
4-3-2/M82	0.79973	0.698
4-3/M82	0.72864	0.366
5-3/M82	0.97242	0.642
6-2/M82	0.9515	1
6-3/M82	0.9232	1
7-1/M82	0.94772	0.803
7-2/M82	1.03713	1
9-3-2/M82	0.71808	0.355

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.2295	0.321
IL2-6/WTpooled	0.99325	1
IL7-5/WTpooled	0.62639	1
IL7-3/WTpooled	0.7119	0.294
IL12-4/WTpooled	1.05086	1
IL1-4/WTpooled	0.92646	0.834
WT/WTpooled	0.97472	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	0.95708

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.01881	0.914
DC3000/delta hrp 6h	1.10766
DC3000/delta hrp 12h	1.18037	1
DC3000/delta hrp 24h	1.04696	0.502

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.904
DC3000 delta B/DC3000 delta AB	1.1364	0.377

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	1.02278	1
Var 0h	1.00018	1
Var 12h I row2-row1	1.07418	0.473
Var 12h NI row2-row1	0.84753	0.488
Var 36h I row2-row1	0.89223	0.805
Var 36h NI row2-row1	0.9235	0.706
Var 60h I row2-row1	1.15698	0.271
Var 60h NI row2-row1	0.98657	1
Time course 0hI-0hNI	1.01911	0.852
Time course 12hI-12hNI	0.97622	0.782
Time course 36hI-36hNI	0.82483	0.053
Time course 60hI-60hNI	0.856	0.161

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)	N/A	N/A
transgenic ySAMdc/azygous control (breaker)	N/A	N/A
transgenic ySAMdc/azygous control (red)	N/A	N/A

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.02439	0.372

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.89596	0.241

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	N/A	N/A
Manapal/WT (break)	N/A	N/A
Manapal/WT (red)	N/A	N/A