Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.1.3.9

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.65735	0.067
27DAP/17DAP	1.22137	0.785
39DAP/27DAP	1.08405	0.853
41DAP/39DAP	0.97669	0.83
42DAP/41DAP	1.15095	0.877
43DAP/42DAP	0.86143	0.495
47DAP/43DAP	0.81694	0.449
52DAP/47DAP	1.83064	0.193
57DAP/52DAP	0.8618	0.85

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.54033	0.008
17DAP/reference	0.97684	0.737
27DAP/reference	0.95001	0.349
39DAP/reference	0.81042	0.234
41DAP/reference	0.9036	0.114
42DAP/reference	1.32745	0.015
43DAP/reference	1.28263
47DAP/reference	1.17787	0.04
52DAP/reference	1.90165	0.009
57DAP/reference	0.79678

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.82258	0.068
27DAP/17DAP	0.9417	0.475
39DAP/27DAP	0.94777	0.587
41DAP/39DAP	1.15146	0.393
42DAP/41DAP	0.85173	0.044
43DAP/42DAP	1.16061	0.147
47DAP/43DAP	1.07237	0.65
52DAP/47DAP	1.09078	0.689
57DAP/52DAP	1.54622	0.067
57DAP/7DAP	1.21923	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.09778	0.472
17DAP/reference	0.91772	0.064
27DAP/reference	0.92778	0.035
39DAP/reference	0.9177	0.012
41DAP/reference	0.96437	0.449
42DAP/reference	0.99464	0.713
43DAP/reference	1.07905	0.178
47DAP/reference	1.03366	0.868
52DAP/reference	1.03033	0.563
57DAP/reference	1.00478	1

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.42662	0.049
17DAP/reference	1.42919	0.033
27DAP/reference	1.79403	0.02
39DAP/reference	1.33732	0.017
41DAP/reference	1.56334	0.01
42DAP/reference	1.46479	0.013
43DAP/reference	1.23219	0.188
47DAP/reference	1.38106	0.019
52DAP/reference	1.02765	0.882
57DAP/reference	1.12489	0.306

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.0837	0.518
17DAP/reference	1.05263	0.728
27DAP/reference	1.04364	0.467
39DAP/reference	1.00229	0.889
41DAP/reference	0.93559	0.237
42DAP/reference	1.02343	1
43DAP/reference	1.14476	0.572
47DAP/reference	1.12702	0.265
52DAP/reference	1.07471	0.649
57DAP/reference	2.31024	0.009

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.16942	0.966
26DAP/20DAP	0.92926	0.512
34DAP/26DAP	0.87266	0.399
51DAP/34DAP	0.87624	0.22
52DAP/51DAP	1.01858	0.836
53DAP/52DAP	1.06151	0.552
55DAP/53DAP	1.04932	0.737
57DAP/55DAP	0.99619	0.904
62DAP/57DAP	0.3514
68DAP/62DAP	0.82601	0.769
68DAP/14DAP	1.28347

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.36804	0.052

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.07487	0.417
Mature Green Tomato/Ripe Tomato	0.59991	0.027
Immature Eggplant/Mature Eggplant	0.73488	0.064
Ripe Pepper/Ripe Tomato	0.41415	0.293
Mature Eggplant/Ripe Tomato	0.53577	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.92563	0.638
1-1-2/M82	0.93734	1
12-2/M82	1.56596	0.327
12-4/M82	0.98695	1
1-3/M82	0.9451	0.501
2-1-1/M82	1.19902	0.422
2-1/M82	1.57674
2-6/M82	1.16656	0.695
3-2/M82	0.91254	0.428
4-1-1/M82	1.05059	1
4-1/M82	0.83274	1
4-3-2/M82	0.817	1
4-3/M82	0.81429	0.72
5-3/M82	0.84079	0.642
6-2/M82	0.96261	1
6-3/M82	0.956	1
7-1/M82	1.05213	1
7-2/M82	1.01701	1
9-3-2/M82	0.80124	0.355

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	0.67185
IL1-4/WTpooled	0.92736	0.834
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	1.32916	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.04024	0.921
DC3000/delta hrp 6h	0.93589	0.95
DC3000/delta hrp 12h	1.247	1
DC3000/delta hrp 24h	1.06191	0.347

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.1122
DC3000 delta B/DC3000 delta AB	1.02276	0.687

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.82003	1
Exp 36h	1.21503	0.489
Exp 60h	1.28866	0.399

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

hybridization	ratio	FDR (corrected p value)
self-self	0.96233	1
Var 0h	1.21323	0.421
Var 12h I row2-row1	1.10624	0.58
Var 12h NI row2-row1	0.92873	0.713
Var 36h I row2-row1	0.93229	0.805
Var 36h NI row2-row1	0.82705	0.549
Var 60h I row2-row1	1.1176	1
Var 60h NI row2-row1	1.15027	0.904
Time course 0hI-0hNI	1.04639	0.799
Time course 12hI-12hNI	1.03	0.747
Time course 36hI-36hNI	1.22908	0.007
Time course 60hI-60hNI	1.35173	0.009

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)	1.23363	0.321
transgenic ySAMdc/azygous control (breaker)	1.06967	1
transgenic ySAMdc/azygous control (red)	0.93783	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.18544	0.042

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.67753	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.01642	1
Manapal/WT (break)	0.77865	1
Manapal/WT (red)	1.44123	0.413