Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.2.16.1

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.55544	0.023
27DAP/17DAP	1.00556	1
39DAP/27DAP	1.47483	0.293
41DAP/39DAP	1.20664	0.58
42DAP/41DAP	1.2262	0.681
43DAP/42DAP	1.15167	0.991
47DAP/43DAP	0.76129	0.308
52DAP/47DAP	1.26482	0.879
57DAP/52DAP	0.88167	0.908

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.17302	0.334
17DAP/reference	0.94186	0.393
27DAP/reference	1.00211	0.867
39DAP/reference	0.81204	0.088
41DAP/reference	0.78467	0.039
42DAP/reference	0.8372	0.025
43DAP/reference	0.96617	0.611
47DAP/reference	0.90547	0.148
52DAP/reference	0.96384	0.438
57DAP/reference	1.27034	0.039

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.15627	0.675
27DAP/17DAP	0.98641	0.943
39DAP/27DAP	1.38987	0.394
41DAP/39DAP	1.24943	0.469
42DAP/41DAP	0.94712	0.584
43DAP/42DAP	1.25093	0.112
47DAP/43DAP	1.69153	0.017
52DAP/47DAP	0.88812	0.694
57DAP/52DAP	1.53848	0.06
57DAP/7DAP	3.48698	0.249

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.92252	0.296
17DAP/reference	1.00915	0.693
27DAP/reference	0.99557	0.698
39DAP/reference	0.80853	0.031
41DAP/reference	0.74612	0.019
42DAP/reference	0.71221	0.01
43DAP/reference	0.84362	0.042
47DAP/reference	0.87592	0.168
52DAP/reference	0.85607	0.053
57DAP/reference	0.78958	0.093

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.84544	0.257
17DAP/reference	0.81904	0.134
27DAP/reference	0.89567	0.257
39DAP/reference	0.91919	0.168
41DAP/reference	0.91217	0.164
42DAP/reference	0.91354	0.237
43DAP/reference	0.74482	0.056
47DAP/reference	0.71384	0.012
52DAP/reference	0.92776	0.239
57DAP/reference	0.69187	0.005

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.03555	0.939
17DAP/reference	0.95474	0.508
27DAP/reference	1.02717	0.749
39DAP/reference	0.97001	0.504
41DAP/reference	1.04585	1
42DAP/reference	1.0558	0.789
43DAP/reference	1.11853	0.482
47DAP/reference	0.86315	0.097
52DAP/reference	0.999	0.732
57DAP/reference	1.0251	1

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.0669	1
26DAP/20DAP	1.11922	1
34DAP/26DAP	1.99787	0.819
51DAP/34DAP	1.375
52DAP/51DAP	1.00512	1
53DAP/52DAP	1.36446	0.129
55DAP/53DAP	1.57857	0.16
57DAP/55DAP	1.33773	0.93
62DAP/57DAP	1.35447	0.833
68DAP/62DAP	1.23882	0.8
68DAP/14DAP	4.3118

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.50961	0.052

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.96849	0.715
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	0.65713
1-1-2/M82	N/A	N/A
12-2/M82	N/A	N/A
12-4/M82	0.95099	1
1-3/M82	0.64048
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	1.06034
4-3/M82	N/A	N/A
5-3/M82	0.7332	0.374
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	N/A	N/A
IL2-6/WTpooled	0.94769	1
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.03892	1
IL12-4/WTpooled	1.13926	0.52
IL1-4/WTpooled	0.94079	0.834
WT/WTpooled	0.97747	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	0.96746	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.04947	0.914
DC3000/delta hrp 6h	1.26943	1
DC3000/delta hrp 12h	0.98439	1
DC3000/delta hrp 24h	1.78026	0.03

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	2.41385
DC3000 delta B/DC3000 delta AB	1.14852	0.336

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.58437	0.328
Exp 36h	0.39226	0.406
Exp 60h	0.60474	0.278

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

hybridization	ratio	FDR (corrected p value)
self-self	0.99611	1
Var 0h	0.85518	0.933
Var 12h I row2-row1	1.15996	0.613
Var 12h NI row2-row1	1.1934	0.649
Var 36h I row2-row1	0.84857	0.805
Var 36h NI row2-row1	0.83022	0.549
Var 60h I row2-row1	0.76336	0.582
Var 60h NI row2-row1	0.96624	0.977
Time course 0hI-0hNI	1.08052	0.574
Time course 12hI-12hNI	0.93768	0.426
Time course 36hI-36hNI	1.03977	0.874
Time course 60hI-60hNI	1.56098	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)	2.85201	0.921
transgenic ySAMdc/azygous control (breaker)	1.16333	1
transgenic ySAMdc/azygous control (red)	1.27517	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.11106	0.044

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.07274	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.61658	0.172
Manapal/WT (break)	1.053	1
Manapal/WT (red)	0.82428	0.216