Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.3.7.8

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.18525	0.403
27DAP/17DAP	0.85621	0.626
39DAP/27DAP	1.10282	0.91
41DAP/39DAP	0.75853	0.183
42DAP/41DAP	0.79464	0.774
43DAP/42DAP	0.86773	0.698
47DAP/43DAP	0.75375	0.29
52DAP/47DAP	0.79587	0.508
57DAP/52DAP	0.81301	0.82

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.15427	0.23
17DAP/reference	1.16252	0.258
27DAP/reference	1.58293	0.01
39DAP/reference	1.59546	0.018
41DAP/reference	1.1423	0.338
42DAP/reference	1.15623	0.005
43DAP/reference	1.03452	0.596
47DAP/reference	0.99664	0.636
52DAP/reference	1.22372	0.062
57DAP/reference	1.44359	0.082

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.18554	0.111
27DAP/17DAP	0.96402	0.887
39DAP/27DAP	0.77815	0.057
41DAP/39DAP	0.96129	0.973
42DAP/41DAP	0.87137	0.153
43DAP/42DAP	0.89489	0.165
47DAP/43DAP	0.7869	0.039
52DAP/47DAP	1.30108	0.498
57DAP/52DAP	0.78338	0.104
57DAP/7DAP	0.6076	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.26888	0.049
17DAP/reference	1.1981	0.016
27DAP/reference	1.30187	0.012
39DAP/reference	1.11988	0.351
41DAP/reference	0.76664	0.046
42DAP/reference	1.2552	0.037
43DAP/reference	0.97555	0.459
47DAP/reference	0.82927	0.036
52DAP/reference	1.09462	0.229
57DAP/reference	1.25394	0.046

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.18799	0.416
17DAP/reference	1.30815	0.094
27DAP/reference	1.31739	0.034
39DAP/reference	1.05547	0.912
41DAP/reference	1.10795	0.172
42DAP/reference	1.46473	0.008
43DAP/reference	1.36876	0.09
47DAP/reference	1.36427	0.013
52DAP/reference	1.11706	0.444
57DAP/reference	0.78055	0.04

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.24903	0.034
17DAP/reference	1.79612	0.139
27DAP/reference	1.55301	0.018
39DAP/reference	1.64824	0.006
41DAP/reference	1.50723	0.028
42DAP/reference	1.50208	0.011
43DAP/reference	1.29221	0.214
47DAP/reference	1.35522	0.03
52DAP/reference	1.03097	0.862
57DAP/reference	1.63297	0.015

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.89851	1
26DAP/20DAP	0.91697	1
34DAP/26DAP	1.24548	0.092
51DAP/34DAP	0.92841	0.631
52DAP/51DAP	0.87381	1
53DAP/52DAP	1.02153	1
55DAP/53DAP	1.12021	0.938
57DAP/55DAP	0.66699	0.238
62DAP/57DAP	1.16849	0.833
68DAP/62DAP	1.09588	0.788
68DAP/14DAP	1.18135	0.346

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.92689	0.015

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	3.80855	0.058
Mature Green Tomato/Ripe Tomato	6.49848	0.015
Immature Eggplant/Mature Eggplant	0.47781	0.062
Ripe Pepper/Ripe Tomato	1.51307	1
Mature Eggplant/Ripe Tomato	8.30288	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.15564	0.742
1-1-2/M82	1.00063	1
12-2/M82	1.34936	0.61
12-4/M82	1.02951	1
1-3/M82	1.14394	1
2-1-1/M82	0.78008
2-1/M82	N/A	N/A
2-6/M82	0.95835	1
3-2/M82	0.95366	1
4-1-1/M82	0.74983	1
4-1/M82	1.25223
4-3-2/M82	0.85857
4-3/M82	N/A	N/A
5-3/M82	1.03025	1
6-2/M82	0.87449
6-3/M82	0.96459	1
7-1/M82	N/A	N/A
7-2/M82	0.93518	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	1.01388	1
IL2-6/WTpooled	1.04944	1
IL7-5/WTpooled	0.68092
IL7-3/WTpooled	0.8415	0.294
IL12-4/WTpooled	0.95054	1
IL1-4/WTpooled	0.93682	0.476
WT/WTpooled	0.9897	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	0.90968	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.95362	1
DC3000/delta hrp 6h	1.08324	1
DC3000/delta hrp 12h	0.90262	1
DC3000/delta hrp 24h	0.84804	0.057

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.63459	0.024
DC3000 delta B/DC3000 delta AB	0.61766	0.031

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	1.02379	1
Var 0h	1.24549	0.311
Var 12h I row2-row1	0.80789	0.338
Var 12h NI row2-row1	0.90161	0.627
Var 36h I row2-row1	1.20989	1
Var 36h NI row2-row1	1.11059	0.482
Var 60h I row2-row1	0.84345	0.293
Var 60h NI row2-row1	0.97305	1
Time course 0hI-0hNI	1.01572	0.852
Time course 12hI-12hNI	0.91027	0.142
Time course 36hI-36hNI	0.81551	0.054
Time course 60hI-60hNI	0.27849	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)	0.98209	0.428
transgenic ySAMdc/azygous control (breaker)	1.54232	0.248
transgenic ySAMdc/azygous control (red)	1.79516	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.00431	0.811

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.26461	0.222

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	2.68345	0.088
Manapal/WT (break)	4.64454	0.126
Manapal/WT (red)	5.29327	0.142