Tomato Functional Genomics Database (TFGD)

Expression of 1-1-8.3.5.7

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.80259	0.217
27DAP/17DAP	0.82251	0.483
39DAP/27DAP	1.22755	0.447
41DAP/39DAP	1.26119	0.293
42DAP/41DAP	1.74305	0.1
43DAP/42DAP	1.21441	0.726
47DAP/43DAP	0.61963	0.079
52DAP/47DAP	0.64114	0.141
57DAP/52DAP	1.19668	0.977

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.22436	0.154
17DAP/reference	1.09823	0.33
27DAP/reference	0.944	0.406
39DAP/reference	1.01726	0.889
41DAP/reference	1.09148	0.393
42DAP/reference	1.19594	0.014
43DAP/reference	1.19968	0.306
47DAP/reference	1.09282	0.295
52DAP/reference	1.03078	1
57DAP/reference	0.91543	0.096

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.95199	0.629
27DAP/17DAP	0.80537	0.446
39DAP/27DAP	1.41624	0.147
41DAP/39DAP	0.61504	0.019
42DAP/41DAP	1.57757	0.139
43DAP/42DAP	2.14715	0.013
47DAP/43DAP	0.78149	0.029
52DAP/47DAP	1.04454	0.831
57DAP/52DAP	0.7449	0.06
57DAP/7DAP	0.84164	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.91083	0.27
17DAP/reference	0.73559	0.013
27DAP/reference	0.89119	0.071
39DAP/reference	0.74132	0.013
41DAP/reference	0.7449	0.021
42DAP/reference	0.63522	0.01
43DAP/reference	0.7112	0.02
47DAP/reference	0.92089	0.293
52DAP/reference	0.66561	0.021
57DAP/reference	0.67324	0.006

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.1902	0.325
17DAP/reference	1.19933	0.03
27DAP/reference	1.18877	0.102
39DAP/reference	0.98382	0.586
41DAP/reference	0.92658	0.299
42DAP/reference	0.96032	0.392
43DAP/reference	1.29135	0.137
47DAP/reference	0.96942	0.41
52DAP/reference	1.11261	0.007
57DAP/reference	1.10598	0.827

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.82493	0.065
17DAP/reference	0.93326	0.462
27DAP/reference	0.67875	0.025
39DAP/reference	0.76049	0.016
41DAP/reference	0.85112	0.086
42DAP/reference	0.94683	0.445
43DAP/reference	1.10412	0.973
47DAP/reference	0.9526	0.259
52DAP/reference	1.02371	0.8
57DAP/reference	1.06293	0.924

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.30154	0.916
26DAP/20DAP	0.86911	1
34DAP/26DAP	0.97645
51DAP/34DAP	1.12629
52DAP/51DAP	1.03041	1
53DAP/52DAP	1.22952	0.91
55DAP/53DAP	0.62557	0.233
57DAP/55DAP	1.07705	0.97
62DAP/57DAP	1.14715	0.833
68DAP/62DAP	0.82669	0.579
68DAP/14DAP	0.66871	0.375

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	2.25638	0.02

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.63017	0.149
Mature Green Tomato/Ripe Tomato	0.93919	0.522
Immature Eggplant/Mature Eggplant	0.77584	0.254
Ripe Pepper/Ripe Tomato	1.31295	0.258
Mature Eggplant/Ripe Tomato	0.91587	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.13102	1
1-1-2/M82	1.09666	1
12-2/M82	0.77219
12-4/M82	1.30073	1
1-3/M82	N/A	N/A
2-1-1/M82	1.12215	0.375
2-1/M82	N/A	N/A
2-6/M82	1.03672
3-2/M82	1.22025
4-1-1/M82	0.83389	1
4-1/M82	2.33034	0.512
4-3-2/M82	1.71499	0.284
4-3/M82	1.19978
5-3/M82	1.07505	1
6-2/M82	N/A	N/A
6-3/M82	0.83446
7-1/M82	0.91209	0.803
7-2/M82	N/A	N/A
9-3-2/M82	1.57471	0.196

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.0765	0.277
IL2-6/WTpooled	0.99126	1
IL7-5/WTpooled	1.27891	0.792
IL7-3/WTpooled	1.02829	1
IL12-4/WTpooled	1.04048	0.891
IL1-4/WTpooled	1.11851	1
WT/WTpooled	0.93615	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	0.88749	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.92251	0.941
DC3000/delta hrp 6h	0.98947	0.95
DC3000/delta hrp 12h	1.05977	1
DC3000/delta hrp 24h	1.0533	0.502

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.06629	0.598
DC3000 delta B/DC3000 delta AB	1.04875	0.726

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.90264	1
Exp 36h	0.99005	1
Exp 60h	1.03824	1

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

hybridization	ratio	FDR (corrected p value)
self-self	1.06346	1
Var 0h	0.7538	1
Var 12h I row2-row1	0.83088	0.31
Var 12h NI row2-row1	0.98239	1
Var 36h I row2-row1	0.81711	1
Var 36h NI row2-row1	1.1385	1
Var 60h I row2-row1	0.93919	0.832
Var 60h NI row2-row1	0.96518	0.977
Time course 0hI-0hNI	0.92312	0.433
Time course 12hI-12hNI	1.05165	0.709
Time course 36hI-36hNI	0.85602	0.057
Time course 60hI-60hNI	0.53888	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)	1.02708	0.654
transgenic ySAMdc/azygous control (breaker)	1.79908	0.162
transgenic ySAMdc/azygous control (red)	1.11654	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.96371	0.143

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.05955	0.233

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.54233	0.083
Manapal/WT (break)	1.48271	0.381
Manapal/WT (red)	1.46384	0.222