Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.2.15.18

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	9.6935	0.019
27DAP/17DAP	1.74853	0.606
39DAP/27DAP	2.02749	0.028
41DAP/39DAP	0.65652	0.123
42DAP/41DAP	1.75385	0.903
43DAP/42DAP	1.69463	0.835
47DAP/43DAP	1.22654	0.889
52DAP/47DAP	1.12452	0.634
57DAP/52DAP	3.12648	0.946

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.87451	0.194
17DAP/reference	1.85837	0.029
27DAP/reference	2.52638	0.033
39DAP/reference	2.79329	0.012
41DAP/reference	2.8534	0.012
42DAP/reference	3.69724	0.001
43DAP/reference	3.06011	0.006
47DAP/reference	5.57864	0.001
52DAP/reference	1.64291	0.033
57DAP/reference	1.67295	0.018

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	2.33633	0.036
27DAP/17DAP	1.52437	0.287
39DAP/27DAP	1.13043	0.548
41DAP/39DAP	1.41533	0.868
42DAP/41DAP	0.99452	0.679
43DAP/42DAP	1.23268	0.554
47DAP/43DAP	1.10217	0.95
52DAP/47DAP	1.34158	0.703
57DAP/52DAP	0.82141	0.349
57DAP/7DAP	5.12347	0.23

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.94508	0.495
17DAP/reference	1.45315	0.007
27DAP/reference	1.23299	0.107
39DAP/reference	1.97254	0.006
41DAP/reference	2.18689	0.008
42DAP/reference	3.40591	0.006
43DAP/reference	3.87451	0.006
47DAP/reference	3.5803	0.014
52DAP/reference	3.76911	0.007
57DAP/reference	3.48711	0.004

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.53237	0.105
17DAP/reference	2.77443	0.01
27DAP/reference	1.5538	0.042
39DAP/reference	1.98414	0.011
41DAP/reference	1.84918	0.053
42DAP/reference	2.72698	0.007
43DAP/reference	1.57201	0.356
47DAP/reference	2.38554	0.009
52DAP/reference	2.01774	0.014
57DAP/reference	1.53837	0.051

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.47913	0.034
17DAP/reference	1.05102	0.824
27DAP/reference	1.23933	0.056
39DAP/reference	1.7718	0.006
41DAP/reference	1.08108	0.657
42DAP/reference	2.05037	0.007
43DAP/reference	1.7464	0.035
47DAP/reference	3.97901	0.005
52DAP/reference	2.92737	0.029
57DAP/reference	1.84672	0.013

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.71282	0.012
26DAP/20DAP	1.34283	0.312
34DAP/26DAP	0.64937	0.093
51DAP/34DAP	0.41199	0.061
52DAP/51DAP	0.9816	1
53DAP/52DAP	1.72575	0.052
55DAP/53DAP	0.84626	0.233
57DAP/55DAP	1.21109	0.682
62DAP/57DAP	0.77761	0.088
68DAP/62DAP	1.90397	0.455
68DAP/14DAP	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	20.6125	0.014

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	2.26327	0.068
Mature Green Tomato/Ripe Tomato	1.62131	0.07
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	1.34838
Mature Eggplant/Ripe Tomato	1.50379	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.45643	0.503
1-1-2/M82	1.39571	1
12-2/M82	N/A	N/A
12-4/M82	1.34118	1
1-3/M82	1.72002	0.248
2-1-1/M82	0.83214	0.465
2-1/M82	0.47568
2-6/M82	0.57421	1
3-2/M82	N/A	N/A
4-1-1/M82	0.89706	1
4-1/M82	0.80704
4-3-2/M82	1.02537	1
4-3/M82	0.90026	1
5-3/M82	1.34789	0.572
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	1.10145
7-2/M82	0.70228
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.86023	1
IL2-6/WTpooled	2.45689	0.427
IL7-5/WTpooled	0.73856	1
IL7-3/WTpooled	0.58732	0.31
IL12-4/WTpooled	0.97734	1
IL1-4/WTpooled	1.04298	1
WT/WTpooled	0.99948	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	1.12064	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.02545	1
DC3000/delta hrp 6h	0.60401
DC3000/delta hrp 12h	0.86655	1
DC3000/delta hrp 24h	0.60353	0.034

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	N/A	N/A
DC3000 delta B/DC3000 delta AB	0.84008

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.12262	1
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	0.97966	1
Var 0h	1.55513	0.98
Var 12h I row2-row1	0.97679	0.948
Var 12h NI row2-row1	1.34841	1
Var 36h I row2-row1	1.1933	0.489
Var 36h NI row2-row1	1.07556	1
Var 60h I row2-row1	1.172	1
Var 60h NI row2-row1	0.72771	0.63
Time course 0hI-0hNI	1.01156	1
Time course 12hI-12hNI	1.16056	0.164
Time course 36hI-36hNI	1.49844	0.005
Time course 60hI-60hNI	9.18043	0.008

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)	1.01326	0.863
transgenic ySAMdc/azygous control (breaker)	0.6395	0.15
transgenic ySAMdc/azygous control (red)	0.69718	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.94097	0.055

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.52325	0.238

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)	1.02374	1
Manapal/WT (red)	1.71479	1