Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.1.3.6

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.49195	0.014
27DAP/17DAP	0.57475	0.101
39DAP/27DAP	1.21382	0.782
41DAP/39DAP	0.40503	0.041
42DAP/41DAP	0.87394	1
43DAP/42DAP	1.38724	0.402
47DAP/43DAP	0.54386	0.086
52DAP/47DAP	0.56429	0.146
57DAP/52DAP	1.15545	0.993

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	2.19402	0.012
17DAP/reference	1.80654	0.011
27DAP/reference	1.85013	0.009
39DAP/reference	0.33809	0.005
41DAP/reference	0.52964	0.009
42DAP/reference	0.76881	0.045
43DAP/reference	0.39099
47DAP/reference	0.43714	0.001
52DAP/reference	0.35844	0.012
57DAP/reference	N/A	N/A

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.51975	0.034
27DAP/17DAP	1.23709	0.699
39DAP/27DAP	0.46729	0.032
41DAP/39DAP	0.25607	0.013
42DAP/41DAP	1.1379	0.991
43DAP/42DAP	1.99116	0.013
47DAP/43DAP	0.50843	0.008
52DAP/47DAP	0.77211	0.553
57DAP/52DAP	0.83935	0.461
57DAP/7DAP	0.18433	0.145

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	2.53339	0.024
17DAP/reference	1.43743	0.028
27DAP/reference	0.99369	0.656
39DAP/reference	0.85515	0.354
41DAP/reference	0.64045	0.022
42DAP/reference	0.8014	0.106
43DAP/reference	0.6247	0.013
47DAP/reference	0.52575	0.033
52DAP/reference	0.48719	0.011
57DAP/reference	0.61972	0.006

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.1008	0.55
17DAP/reference	1.7528	0.147
27DAP/reference	1.25645	0.38
39DAP/reference	0.70707	0.072
41DAP/reference	0.90231	0.164
42DAP/reference	1.27152	0.398
43DAP/reference	0.45712	0.002
47DAP/reference	0.59757	0.008
52DAP/reference	0.59909	0.006
57DAP/reference	0.48118	0.003

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	3.77952	0.015
17DAP/reference	1.90858	0.168
27DAP/reference	2.02616	0.016
39DAP/reference	0.91816	0.246
41DAP/reference	0.85037	0.185
42DAP/reference	0.7916	0.108
43DAP/reference	0.67839	0.031
47DAP/reference	0.56029	0.005
52DAP/reference	0.79755	0.238
57DAP/reference	1.11654	0.744

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.89006	1
26DAP/20DAP	0.92714	1
34DAP/26DAP	1.11773	1
51DAP/34DAP	0.43528	0.053
52DAP/51DAP	1.01164	1
53DAP/52DAP	0.63088	0.049
55DAP/53DAP	0.4264	0.016
57DAP/55DAP	0.83527	0.398
62DAP/57DAP	1.1929	0.007
68DAP/62DAP	1.19404	0.565
68DAP/14DAP	0.45532	0.075

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.12972	0.019

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.68378	0.058
Mature Green Tomato/Ripe Tomato	11.4951	0.015
Immature Eggplant/Mature Eggplant	0.61411	0.084
Ripe Pepper/Ripe Tomato	21.2975	0.239
Mature Eggplant/Ripe Tomato	42.4608	0.26

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	0.86051	0.619
1-3/M82	N/A	N/A
2-1-1/M82	1.50959
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	1.1042	0.496
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	0.97009	1
IL2-6/WTpooled	1.04406	1
IL7-5/WTpooled	0.99887	1
IL7-3/WTpooled	1.11836	1
IL12-4/WTpooled	1.12627	0.839
IL1-4/WTpooled	0.98722	1
WT/WTpooled	0.99446	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	0.97629	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.92628	1
DC3000/delta hrp 6h	0.97382	0.95
DC3000/delta hrp 12h	1.28933	1
DC3000/delta hrp 24h	0.81712	0.313

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.45188	0.024
DC3000 delta B/DC3000 delta AB	0.45165	0.02

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.9948	1
Exp 36h	0.71911	0.449
Exp 60h	0.76208	0.251

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

hybridization	ratio	FDR (corrected p value)
self-self	1.15732
Var 0h	N/A	N/A
Var 12h I row2-row1	0.72035
Var 12h NI row2-row1	N/A	N/A
Var 36h I row2-row1	1.05398	1
Var 36h NI row2-row1	N/A	N/A
Var 60h I row2-row1	N/A	N/A
Var 60h NI row2-row1	N/A	N/A
Time course 0hI-0hNI	1.11042	0.63
Time course 12hI-12hNI	0.97636	0.924
Time course 36hI-36hNI	0.78529	0.036
Time course 60hI-60hNI	0.1034	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)	0.73374	0.314
transgenic ySAMdc/azygous control (breaker)	2.30376	1
transgenic ySAMdc/azygous control (red)	1.70876	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.46249	0.062

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	4.08935	0.239

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.11094	1
Manapal/WT (break)	2.55837	0.381
Manapal/WT (red)	1.65222	1