Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.4.14.4

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.96384	0.722
27DAP/17DAP	0.74606	0.359
39DAP/27DAP	1.61324	0.208
41DAP/39DAP	1.08592	0.387
42DAP/41DAP	1.27014	0.556
43DAP/42DAP	1.45734	0.148
47DAP/43DAP	0.782	0.369
52DAP/47DAP	0.80272	0.54
57DAP/52DAP	0.91254	0.85

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.43968	0.009
17DAP/reference	1.31052	0.015
27DAP/reference	1.21776	0.027
39DAP/reference	1.16991	0.037
41DAP/reference	1.39354	0.013
42DAP/reference	1.12925	0.338
43DAP/reference	0.92558	0.331
47DAP/reference	0.96991	0.392
52DAP/reference	0.95624	0.393
57DAP/reference	0.82813	0.091

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.09916	0.65
27DAP/17DAP	0.9816	0.919
39DAP/27DAP	1.03182	0.854
41DAP/39DAP	0.83915	0.186
42DAP/41DAP	1.19064	0.478
43DAP/42DAP	1.35873	0.015
47DAP/43DAP	0.97401	0.877
52DAP/47DAP	1.27137	0.317
57DAP/52DAP	1.17038	0.523
57DAP/7DAP	1.16637	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.0864	0.83
17DAP/reference	0.97828	0.518
27DAP/reference	0.8413	0.015
39DAP/reference	1.03531	1
41DAP/reference	1.06453	0.491
42DAP/reference	1.19995	0.1
43DAP/reference	1.16706	0.364
47DAP/reference	0.85252	0.222
52DAP/reference	1.15857	0.266
57DAP/reference	1.10334	0.308

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.275	0.167
17DAP/reference	1.65903	0.01
27DAP/reference	1.40397	0.063
39DAP/reference	1.39278	0.042
41DAP/reference	1.27936	0.024
42DAP/reference	1.40578	0.035
43DAP/reference	1.34824	0.112
47DAP/reference	1.22774	0.009
52DAP/reference	1.38305	0.01
57DAP/reference	1.51237	0.008

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.07548	0.793
17DAP/reference	1.28566	0.436
27DAP/reference	0.93322	0.286
39DAP/reference	0.8733	0.026
41DAP/reference	1.03644	1
42DAP/reference	1.13259	0.459
43DAP/reference	1.17507	0.744
47DAP/reference	0.84947	0.12
52DAP/reference	0.87238	0.166
57DAP/reference	1.09466	0.694

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.62292	0.193
26DAP/20DAP	1.57562	0.136
34DAP/26DAP	1.79943	0.304
51DAP/34DAP	9.89749	0.016
52DAP/51DAP	0.65398	0.151
53DAP/52DAP	2.51921	0.029
55DAP/53DAP	0.79019	0.13
57DAP/55DAP	1.72564	0.34
62DAP/57DAP	1.00189	0.994
68DAP/62DAP	0.7162	0.314
68DAP/14DAP	0.61791	0.375

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.06772	0.019

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.95112	0.569
Immature Eggplant/Mature Eggplant	0.2786	0.057
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	1.56621
12-2/M82	N/A	N/A
12-4/M82	1.22537	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	N/A	N/A
3-2/M82	0.97317
4-1-1/M82	N/A	N/A
4-1/M82	1.94308
4-3-2/M82	1.18239
4-3/M82	N/A	N/A
5-3/M82	0.72453
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	0.65626
7-2/M82	N/A	N/A
9-3-2/M82	1.12783	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.2599
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	1.4267
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	0.99477	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.69514	0.868
DC3000/delta hrp 6h	1.07196	0.95
DC3000/delta hrp 12h	1.09721	1
DC3000/delta hrp 24h	1.0497	0.673

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.61264	0.023
DC3000 delta B/DC3000 delta AB	0.628	0.021

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.92318	1
Exp 36h	0.53313	0.426
Exp 60h	0.5672	0.29

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

hybridization	ratio	FDR (corrected p value)
self-self	1.02027	1
Var 0h	0.94389	1
Var 12h I row2-row1	0.69378	0.338
Var 12h NI row2-row1	0.94217	0.82
Var 36h I row2-row1	0.91024	0.575
Var 36h NI row2-row1	1.26617	0.482
Var 60h I row2-row1	0.96521	0.952
Var 60h NI row2-row1	0.9727	1
Time course 0hI-0hNI	1.0173	1
Time course 12hI-12hNI	0.98455	0.893
Time course 36hI-36hNI	0.83843	0.024
Time course 60hI-60hNI	0.31281	0.006

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)	1.00346	0.931
transgenic ySAMdc/azygous control (breaker)	1.27629	0.178
transgenic ySAMdc/azygous control (red)	0.78189	0.082

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.77363	0.047

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	2.40898	0.231

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	3.23188	0.083
Manapal/WT (break)	2.7055	0.123
Manapal/WT (red)	0.71433	0.242