Tomato Functional Genomics Database (TFGD)

Expression of 1-1-8.2.2.17

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.33734	0.014
27DAP/17DAP	0.45104	0.031
39DAP/27DAP	0.62531	0.378
41DAP/39DAP	0.70922	0.188
42DAP/41DAP	0.61349	0.774
43DAP/42DAP	1.1782	1
47DAP/43DAP	1.11294	0.926
52DAP/47DAP	1.06929	0.823
57DAP/52DAP	1.16644	0.946

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.97616	0.043
17DAP/reference	1.47461	0.014
27DAP/reference	1.85098	0.014
39DAP/reference	0.74663	0.009
41DAP/reference	0.63258	0.008
42DAP/reference	0.81966	0.001
43DAP/reference	0.68986	0.019
47DAP/reference	0.64276	0.001
52DAP/reference	0.64311	0.015
57DAP/reference	0.90048	0.101

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.32742	0.027
27DAP/17DAP	1.0054	1
39DAP/27DAP	0.76875	0.06
41DAP/39DAP	0.59494	0.041
42DAP/41DAP	0.97595	0.797
43DAP/42DAP	1.13194	0.585
47DAP/43DAP	0.89835	0.332
52DAP/47DAP	1.25303	0.823
57DAP/52DAP	1.21656	0.718
57DAP/7DAP	0.30173	0.219

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.87506	0.024
17DAP/reference	1.40083	0.199
27DAP/reference	1.03647	0.698
39DAP/reference	1.2135	0.036
41DAP/reference	1.1016	0.812
42DAP/reference	1.14301	0.534
43DAP/reference	0.90248	0.086
47DAP/reference	0.6437	0.04
52DAP/reference	1.20475	0.062
57DAP/reference	1.06498	0.308

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.59065	0.122
17DAP/reference	1.49111	0.032
27DAP/reference	0.96833	0.467
39DAP/reference	0.57206	0.008
41DAP/reference	0.61811	0.007
42DAP/reference	0.96723	0.482
43DAP/reference	0.7788	0.08
47DAP/reference	0.72185	0.029
52DAP/reference	0.63409	0.005
57DAP/reference	0.73543	0.028

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	2.03956	0.019
17DAP/reference	1.69474	0.037
27DAP/reference	1.26651	0.022
39DAP/reference	1.37351	0.437
41DAP/reference	1.1416	0.605
42DAP/reference	0.97903	0.816
43DAP/reference	1.01862	0.545
47DAP/reference	0.50627	0.004
52DAP/reference	0.76001	0.228
57DAP/reference	0.8603	0.12

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.13744	0.966
26DAP/20DAP	1.34079	0.21
34DAP/26DAP	0.85488	0.247
51DAP/34DAP	0.60358	0.053
52DAP/51DAP	0.86546	0.151
53DAP/52DAP	0.74267	0.08
55DAP/53DAP	0.61431	0.023
57DAP/55DAP	0.56242	0.019
62DAP/57DAP	N/A	N/A
68DAP/62DAP	0.77629	0.345
68DAP/14DAP	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.12608	0.02

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.32692	0.068
Mature Green Tomato/Ripe Tomato	7.55857	0.015
Immature Eggplant/Mature Eggplant	0.42971	0.062
Ripe Pepper/Ripe Tomato	57.9147	0.258
Mature Eggplant/Ripe Tomato	149.763	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.20612
1-1-2/M82	N/A	N/A
12-2/M82	N/A	N/A
12-4/M82	1.1611
1-3/M82	0.98995	1
2-1-1/M82	0.55663
2-1/M82	N/A	N/A
2-6/M82	1.01386	1
3-2/M82	N/A	N/A
4-1-1/M82	0.92572	1
4-1/M82	2.23617
4-3-2/M82	N/A	N/A
4-3/M82	N/A	N/A
5-3/M82	0.94582	1
6-2/M82	N/A	N/A
6-3/M82	1.06853	0.971
7-1/M82	0.86812
7-2/M82	0.90826	0.881
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	0.89931	0.337
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.88683	1
IL12-4/WTpooled	0.92813	1
IL1-4/WTpooled	1.01279
WT/WTpooled	0.93177	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	0.72216	0.341

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.99017	1
DC3000/delta hrp 6h	0.98702	0.95
DC3000/delta hrp 12h	1.16499	1
DC3000/delta hrp 24h	0.77858	0.174

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.37433	0.023
DC3000 delta B/DC3000 delta AB	0.40012	0.02

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.98985	1
Exp 36h	0.68442	0.434
Exp 60h	0.62833	0.257

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

hybridization	ratio	FDR (corrected p value)
self-self	0.97638	1
Var 0h	0.5264	0.226
Var 12h I row2-row1	0.81218	0.31
Var 12h NI row2-row1	0.80604	0.494
Var 36h I row2-row1	0.97492	1
Var 36h NI row2-row1	1.20217	1
Var 60h I row2-row1	1.04622
Var 60h NI row2-row1	1.0387	0.904
Time course 0hI-0hNI	0.97034	0.866
Time course 12hI-12hNI	0.86191	0.149
Time course 36hI-36hNI	0.71732	0.023
Time course 60hI-60hNI	0.07982	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)	0.74988	0.338
transgenic ySAMdc/azygous control (breaker)	1.45524	0.248
transgenic ySAMdc/azygous control (red)	0.90972	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.87653	0.115

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	3.84174	0.237

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.38592	0.14
Manapal/WT (break)	2.23	0.14
Manapal/WT (red)	1.0895	1