Tomato Functional Genomics Database (TFGD)

Expression of 1-1-4.4.13.6

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.01055	0.891
27DAP/17DAP	1.11401	0.881
39DAP/27DAP	0.85408	0.402
41DAP/39DAP	0.69119	0.183
42DAP/41DAP	0.90596	1
43DAP/42DAP	0.84989	0.705
47DAP/43DAP	1.07258	0.825
52DAP/47DAP	1.29923	0.451
57DAP/52DAP	0.89432	0.882

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.87509	0.106
17DAP/reference	0.84903	0.069
27DAP/reference	0.92617	0.295
39DAP/reference	0.93371	0.391
41DAP/reference	0.81052	0.114
42DAP/reference	0.77425	0.001
43DAP/reference	0.93763	0.41
47DAP/reference	0.93724	0.174
52DAP/reference	1.01721	0.991
57DAP/reference	1.23176	0.059

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.04083	0.975
27DAP/17DAP	1.35218	0.9
39DAP/27DAP	1.15327	0.422
41DAP/39DAP	1.02742	0.921
42DAP/41DAP	1.01701	0.887
43DAP/42DAP	1.03857	0.554
47DAP/43DAP	0.9656	0.846
52DAP/47DAP	1.00073	0.975
57DAP/52DAP	0.96622	0.756
57DAP/7DAP	1.32624	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.10877	0.461
17DAP/reference	1.11225	0.361
27DAP/reference	1.13628	0.301
39DAP/reference	1.22609	0.038
41DAP/reference	1.15937	0.291
42DAP/reference	1.14036	0.405
43DAP/reference	1.48801	0.022
47DAP/reference	1.09861	0.685
52DAP/reference	1.1657	0.149
57DAP/reference	1.22379	0.043

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.84521	0.087
17DAP/reference	0.72421	0.012
27DAP/reference	0.76567	0.054
39DAP/reference	0.89644	0.168
41DAP/reference	0.91561	0.237
42DAP/reference	0.83353	0.081
43DAP/reference	0.82851	0.125
47DAP/reference	0.82154	0.012
52DAP/reference	0.94843	0.327
57DAP/reference	0.67047	0.002

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.97114	0.422
17DAP/reference	1.00993	0.87
27DAP/reference	1.33513	0.021
39DAP/reference	1.07366	0.296
41DAP/reference	1.11069	0.125
42DAP/reference	1.01147	1
43DAP/reference	0.90964	0.305
47DAP/reference	0.97752	0.525
52DAP/reference	0.99449	0.838
57DAP/reference	1.03482	0.991

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.00667	1
26DAP/20DAP	0.95737
34DAP/26DAP	6.15863	0.819
51DAP/34DAP	1.82684	0.241
52DAP/51DAP	1.56403	0.503
53DAP/52DAP	0.91571	0.715
55DAP/53DAP	0.89776	0.515
57DAP/55DAP	0.78732	0.202
62DAP/57DAP	0.96432	0.994
68DAP/62DAP	1.72239	0.018
68DAP/14DAP	2.37782	0.087

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.23294	0.954

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.36486	0.017
Immature Eggplant/Mature Eggplant	0.75226
Ripe Pepper/Ripe Tomato	0.34672	0.224
Mature Eggplant/Ripe Tomato	0.38118	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.09793
1-1-2/M82	1.32622
12-2/M82	1.16228
12-4/M82	0.98373	1
1-3/M82	0.95474
2-1-1/M82	0.88568
2-1/M82	1.65587
2-6/M82	0.97919
3-2/M82	0.92744
4-1-1/M82	N/A	N/A
4-1/M82	N/A	N/A
4-3-2/M82	N/A	N/A
4-3/M82	1.28378	1
5-3/M82	1.03115	1
6-2/M82	0.8853
6-3/M82	N/A	N/A
7-1/M82	0.87488
7-2/M82	0.81261
9-3-2/M82	0.8845

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	1.14206	0.531
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.15443	0.362
IL12-4/WTpooled	1.075	0.538
IL1-4/WTpooled	1.16798
WT/WTpooled	0.95048	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	1.02006	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.03524	0.921
DC3000/delta hrp 6h	1.01341	1
DC3000/delta hrp 12h	1.17236	1
DC3000/delta hrp 24h	0.94467	0.598

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	N/A	N/A
Exp 36h	N/A	N/A
Exp 60h	1.07501	1

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

hybridization	ratio	FDR (corrected p value)
self-self	1.07826	1
Var 0h	0.87239
Var 12h I row2-row1	1.16039	0.176
Var 12h NI row2-row1	1.06027	1
Var 36h I row2-row1	2.1549	0.908
Var 36h NI row2-row1	0.34418	1
Var 60h I row2-row1	0.93225	0.374
Var 60h NI row2-row1	0.90674	0.701
Time course 0hI-0hNI	1.02005	1
Time course 12hI-12hNI	1.01326	1
Time course 36hI-36hNI	0.97584	0.549
Time course 60hI-60hNI	0.90505	0.319

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)	0.96556	0.362
transgenic ySAMdc/azygous control (breaker)	1.15768	0.166
transgenic ySAMdc/azygous control (red)	0.89426	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.93228	0.036

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.93065	0.284

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.82558	1
Manapal/WT (break)	0.75829	0.333
Manapal/WT (red)	0.70129	0.181