Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.1.20.16

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.92729	0.464
27DAP/17DAP	2.65334	0.321
39DAP/27DAP	1.20716	0.825
41DAP/39DAP	1.22685	0.663
42DAP/41DAP	1.38743	0.644
43DAP/42DAP	1.22922	1
47DAP/43DAP	0.70531	0.208
52DAP/47DAP	1.05392	0.942
57DAP/52DAP	1.55603	0.839

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.94762	0.442
17DAP/reference	0.94465	0.342
27DAP/reference	1.08954	0.054
39DAP/reference	1.00131	1
41DAP/reference	0.81126	0.026
42DAP/reference	0.95814	0.242
43DAP/reference	1.03624	0.678
47DAP/reference	0.98316	0.473
52DAP/reference	1.09945	0.371
57DAP/reference	1.21798	0.009

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.09082	0.508
27DAP/17DAP	0.96598	0.854
39DAP/27DAP	1.29738	0.099
41DAP/39DAP	0.95537	0.793
42DAP/41DAP	1.00757	1
43DAP/42DAP	0.97035	0.665
47DAP/43DAP	1.16473	0.508
52DAP/47DAP	1.07501	0.734
57DAP/52DAP	1.20909	0.346
57DAP/7DAP	1.00953	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.01	1
17DAP/reference	1.08312	0.077
27DAP/reference	1.07799	0.02
39DAP/reference	1.04697	0.141
41DAP/reference	1.16757	0.014
42DAP/reference	1.11426	0.024
43DAP/reference	1.07845	0.056
47DAP/reference	1.07659	0.337
52DAP/reference	1.03875	0.058
57DAP/reference	1.08811	0.01

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.83257	0.02
17DAP/reference	0.76745	0.006
27DAP/reference	0.81677	0.026
39DAP/reference	0.99901	0.722
41DAP/reference	0.98114	0.57
42DAP/reference	0.85488	0.024
43DAP/reference	0.92186	0.292
47DAP/reference	0.87233	0.126
52DAP/reference	0.95905	0.327
57DAP/reference	0.877	0.063

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.06604	0.366
17DAP/reference	0.90795	0.286
27DAP/reference	1.03213	0.248
39DAP/reference	1.05957	0.057
41DAP/reference	1.06949	0.134
42DAP/reference	0.98314	0.671
43DAP/reference	0.9983	0.827
47DAP/reference	0.98053	0.558
52DAP/reference	1.08829	0.324
57DAP/reference	1.08975	0.304

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.16166	0.966
26DAP/20DAP	1.31514	0.315
34DAP/26DAP	1.17354	0.819
51DAP/34DAP	1.31551	0.281
52DAP/51DAP	0.95584	1
53DAP/52DAP	1.20811	0.413
55DAP/53DAP	1.15776	0.29
57DAP/55DAP	0.87676	0.499
62DAP/57DAP	1.05944	0.8
68DAP/62DAP	1.40543	0.202
68DAP/14DAP	1.4171	0.022

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.96911	0.576

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.13654	0.417
Mature Green Tomato/Ripe Tomato	0.81985	0.018
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	0.89489	1
Mature Eggplant/Ripe Tomato	0.54846	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.91138	0.605
1-1-2/M82	0.96698	1
12-2/M82	0.84268	0.528
12-4/M82	0.86018	0.358
1-3/M82	0.99439
2-1-1/M82	1.20175
2-1/M82	0.86766
2-6/M82	0.94108	1
3-2/M82	1.01696
4-1-1/M82	N/A	N/A
4-1/M82	0.98848
4-3-2/M82	0.94328
4-3/M82	0.8363	0.578
5-3/M82	0.98037	1
6-2/M82	N/A	N/A
6-3/M82	1.01048	1
7-1/M82	0.67896
7-2/M82	1.09018	1
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.04207	0.493
IL2-6/WTpooled	1.08396	0.659
IL7-5/WTpooled	1.04293	0.792
IL7-3/WTpooled	1.29416	1
IL12-4/WTpooled	1.17118	0.553
IL1-4/WTpooled	1.34307	1
WT/WTpooled	1.04976	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	1.01274	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.98183	1
DC3000/delta hrp 6h	0.88059	0.95
DC3000/delta hrp 12h	0.99303	1
DC3000/delta hrp 24h	1.14379	0.254

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	1.26002	0.315

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	N/A	N/A
Exp 36h	1.11524	0.371
Exp 60h	1.18536	0.221

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

hybridization	ratio	FDR (corrected p value)
self-self	0.9944	1
Var 0h	N/A	N/A
Var 12h I row2-row1	0.9486	0.514
Var 12h NI row2-row1	0.98414	1
Var 36h I row2-row1	1.05996	0.304
Var 36h NI row2-row1	0.88929	0.743
Var 60h I row2-row1	1.1079	1
Var 60h NI row2-row1	0.87418	0.977
Time course 0hI-0hNI	1.10167	0.413
Time course 12hI-12hNI	1.04036	0.714
Time course 36hI-36hNI	1.21743	0.028
Time course 60hI-60hNI	1.61476	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)	0.89097	0.285
transgenic ySAMdc/azygous control (breaker)	1.05958	1
transgenic ySAMdc/azygous control (red)	0.90548	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.98805	0.517

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.99195	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.864	1
Manapal/WT (break)	0.69441	0.299
Manapal/WT (red)	0.68565	0.181