Tomato Functional Genomics Database (TFGD)

Expression of 1-1-4.4.20.15

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.23318	0.893
27DAP/17DAP	1.11387	0.847
39DAP/27DAP	0.90565	0.573
41DAP/39DAP	1.57213	0.313
42DAP/41DAP	1.06252	0.994
43DAP/42DAP	0.99373	0.937
47DAP/43DAP	1.02243	0.733
52DAP/47DAP	1.10324	0.879
57DAP/52DAP	1.07314	0.977

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.82268	0.035
17DAP/reference	1.03832	0.342
27DAP/reference	0.9964	0.867
39DAP/reference	0.94992	0.261
41DAP/reference	1.01606	0.855
42DAP/reference	0.90934	0.027
43DAP/reference	0.97549	0.691
47DAP/reference	0.88352	0.042
52DAP/reference	0.8901	0.167
57DAP/reference	0.87011	0.051

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.91768	0.47
27DAP/17DAP	0.84661	0.39
39DAP/27DAP	1.23834	0.182
41DAP/39DAP	1.08615	0.895
42DAP/41DAP	0.88126	0.228
43DAP/42DAP	1.19428	0.019
47DAP/43DAP	1.05036	0.844
52DAP/47DAP	1.23638	0.356
57DAP/52DAP	1.0088	0.905
57DAP/7DAP	1.06817	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.11037	0.776
17DAP/reference	1.14644	1
27DAP/reference	0.70759	0.01
39DAP/reference	0.80953	0.015
41DAP/reference	0.84307	0.021
42DAP/reference	0.70771	0.011
43DAP/reference	0.76696	0.015
47DAP/reference	0.99423	1
52DAP/reference	0.92944	0.254
57DAP/reference	0.87348	0.02

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.76271	0.031
17DAP/reference	0.7151	0.008
27DAP/reference	0.75982	0.054
39DAP/reference	0.82721	0.074
41DAP/reference	0.86108	0.087
42DAP/reference	0.80087	0.089
43DAP/reference	0.74398	0.022
47DAP/reference	0.89968	0.066
52DAP/reference	0.89708	0.051
57DAP/reference	0.83102	0.03

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.8867	0.092
17DAP/reference	0.92919	0.433
27DAP/reference	0.78088	0.036
39DAP/reference	0.73764	0.016
41DAP/reference	0.97478	0.618
42DAP/reference	0.82905	0.071
43DAP/reference	0.88454	0.165
47DAP/reference	1.05234	0.847
52DAP/reference	1.00611	0.763
57DAP/reference	1.07223	0.947

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.21086	0.916
26DAP/20DAP	0.82159	0.317
34DAP/26DAP	1.09854	0.304
51DAP/34DAP	1.09515	0.613
52DAP/51DAP	0.98203	1
53DAP/52DAP	0.92179	0.544
55DAP/53DAP	1.10716	0.737
57DAP/55DAP	0.97605	0.859
62DAP/57DAP	1.25107	0.35
68DAP/62DAP	1.20479	0.353
68DAP/14DAP	1.57407	0.024

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.9033	0.341

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.9139	0.487
Immature Eggplant/Mature Eggplant	1.08573	0.606
Ripe Pepper/Ripe Tomato	0.56862	0.293
Mature Eggplant/Ripe Tomato	0.21665	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	N/A	N/A
12-2/M82	N/A	N/A
12-4/M82	1.04152	1
1-3/M82	N/A	N/A
2-1-1/M82	1.17187
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	1.1552
4-3-2/M82	N/A	N/A
4-3/M82	0.84622
5-3/M82	N/A	N/A
6-2/M82	5.43754	0.253
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	0.88132	0.449

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	N/A	N/A
IL1-4/WTpooled	N/A	N/A
WT/WTpooled	N/A	N/A

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	1.0121	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.60914
DC3000/delta hrp 6h	0.93161	0.95
DC3000/delta hrp 12h	1.02945	1
DC3000/delta hrp 24h	1.21987	0.76

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	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.04106	1
Exp 36h	1.58521	0.409
Exp 60h	1.2018	0.399

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

hybridization	ratio	FDR (corrected p value)
self-self	0.96018	1
Var 0h	N/A	N/A
Var 12h I row2-row1	0.83263	0.353
Var 12h NI row2-row1	1.11133	1
Var 36h I row2-row1	1.29341	0.309
Var 36h NI row2-row1	1.02763	1
Var 60h I row2-row1	0.94989	0.952
Var 60h NI row2-row1	0.97093	1
Time course 0hI-0hNI	0.95692	0.758
Time course 12hI-12hNI	0.99273	1
Time course 36hI-36hNI	1.57812	0.006
Time course 60hI-60hNI	1.52018	0.01

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)	0.9761	0.722
transgenic ySAMdc/azygous control (breaker)	0.39891	0.129
transgenic ySAMdc/azygous control (red)	1.27882	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.05465	0.17

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.67936	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.00356	1
Manapal/WT (break)	0.67528	1
Manapal/WT (red)	0.26708	0.184