Tomato Functional Genomics Database (TFGD)

Expression of 1-1-4.2.15.18

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.00936	0.811
27DAP/17DAP	0.84653	0.604
39DAP/27DAP	1.23786	0.626
41DAP/39DAP	0.99668	0.92
42DAP/41DAP	0.90776	1
43DAP/42DAP	1.19489	0.918
47DAP/43DAP	0.94219	0.705
52DAP/47DAP	0.92816	0.712
57DAP/52DAP	1.15581	0.907

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.13002	0.116
17DAP/reference	1.16368	0.083
27DAP/reference	1.37011	0.19
39DAP/reference	1.14448	0.359
41DAP/reference	1.60887	0.014
42DAP/reference	1.37261	0.001
43DAP/reference	1.16762	0.038
47DAP/reference	1.26532	0.005
52DAP/reference	1.35172	0.186
57DAP/reference	1.24252	0.548

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.12682	0.508
27DAP/17DAP	1.17879	0.403
39DAP/27DAP	1.06341	0.779
41DAP/39DAP	1.01473	0.98
42DAP/41DAP	1.15903	0.478
43DAP/42DAP	0.90879	0.367
47DAP/43DAP	0.99964	0.989
52DAP/47DAP	1.09315	0.804
57DAP/52DAP	1.21387	0.374
57DAP/7DAP	1.29809	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	2.19902	0.024
17DAP/reference	1.22249	0.199
27DAP/reference	0.99799	0.698
39DAP/reference	0.96211	0.474
41DAP/reference	0.98058	0.512
42DAP/reference	1.07689	0.534
43DAP/reference	0.94427	0.139
47DAP/reference	1.22057	0.48
52DAP/reference	0.70272	0.012
57DAP/reference	0.77077	0.013

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.3562	0.049
17DAP/reference	1.44148	0.023
27DAP/reference	1.43131	0.102
39DAP/reference	1.47587	0.025
41DAP/reference	1.55058	0.039
42DAP/reference	1.31663	0.056
43DAP/reference	1.32633	0.457
47DAP/reference	1.43852	0.008
52DAP/reference	1.61267	0.006
57DAP/reference	1.93852	0.008

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	2.35133	0.016
17DAP/reference	1.50546	0.041
27DAP/reference	1.23033	0.043
39DAP/reference	0.94739	0.464
41DAP/reference	0.83632	0.028
42DAP/reference	0.87274	0.287
43DAP/reference	0.9676	0.398
47DAP/reference	1.40284	0.066
52DAP/reference	0.83474	0.277
57DAP/reference	1.08128	0.814

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.06832	1
26DAP/20DAP	1.73742	0.166
34DAP/26DAP	1.03535	1
51DAP/34DAP	2.20278	0.032
52DAP/51DAP	0.90913	1
53DAP/52DAP	1.44787	0.121
55DAP/53DAP	0.72558	0.075
57DAP/55DAP	0.81874	0.305
62DAP/57DAP	1.08564	0.994
68DAP/62DAP	1.23686	0.132
68DAP/14DAP	0.95405	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.12045	0.391

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	1.24311	0.237
Immature Eggplant/Mature Eggplant	N/A	N/A
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	1.79441
12-2/M82	N/A	N/A
12-4/M82	1.17757
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	N/A	N/A
4-1-1/M82	N/A	N/A
4-1/M82	N/A	N/A
4-3-2/M82	0.95558	1
4-3/M82	N/A	N/A
5-3/M82	N/A	N/A
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	1.02738	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	1.02084	1
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.43274	1
IL12-4/WTpooled	0.9316	0.478
IL1-4/WTpooled	0.82354	0.834
WT/WTpooled	0.9957	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	0.94411	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.82	0.868
DC3000/delta hrp 6h	N/A	N/A
DC3000/delta hrp 12h	1.22887	1
DC3000/delta hrp 24h	0.64095	0.035

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.84413	0.027
DC3000 delta B/DC3000 delta AB	1.1029	0.381

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	N/A	N/A
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	1.02143	1
Var 0h	1.07642	0.98
Var 12h I row2-row1	0.99502	1
Var 12h NI row2-row1	1.06121	1
Var 36h I row2-row1	1.16144	0.298
Var 36h NI row2-row1	3.222	1
Var 60h I row2-row1	0.66577	0.285
Var 60h NI row2-row1	1.20163	0.904
Time course 0hI-0hNI	1.03489	0.852
Time course 12hI-12hNI	1.06788	0.55
Time course 36hI-36hNI	1.18524	0.016
Time course 60hI-60hNI	1.33369	0.037

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)	N/A	N/A
transgenic ySAMdc/azygous control (breaker)	N/A	N/A
transgenic ySAMdc/azygous control (red)	N/A	N/A

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.89975	0.122

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.93545	0.59

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)	1.59747	0.14
Manapal/WT (red)	N/A	N/A