Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.3.6.7

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.07316	1
27DAP/17DAP	1.08231	0.922
39DAP/27DAP	0.87159	0.608
41DAP/39DAP	1.24888	0.638
42DAP/41DAP	1.17082	0.755
43DAP/42DAP	1.1617	0.933
47DAP/43DAP	1.02855	0.979
52DAP/47DAP	0.98521	0.938
57DAP/52DAP	0.97836	0.971

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.84059	0.121
17DAP/reference	0.86658	0.069
27DAP/reference	0.96106	0.567
39DAP/reference	0.90536	0.188
41DAP/reference	0.84456	0.049
42DAP/reference	0.92091	0.103
43DAP/reference	0.98203	0.745
47DAP/reference	1.04387	0.666
52DAP/reference	1.02431	0.912
57DAP/reference	1.02007	0.853

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.32809	0.184
27DAP/17DAP	1.05833	0.957
39DAP/27DAP	0.9238	0.456
41DAP/39DAP	0.97606	0.997
42DAP/41DAP	0.92241	0.535
43DAP/42DAP	0.96777	0.729
47DAP/43DAP	0.94446	0.805
52DAP/47DAP	0.89906	0.634
57DAP/52DAP	1.69063	0.434
57DAP/7DAP	1.19473	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.92817	0.402
17DAP/reference	1.03677	1
27DAP/reference	1.01076	0.8
39DAP/reference	1.033	1
41DAP/reference	0.94548	0.259
42DAP/reference	0.90816	0.189
43DAP/reference	0.87126	0.241
47DAP/reference	0.94763	0.671
52DAP/reference	1.0225	0.941
57DAP/reference	1.06163	0.799

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.99352	0.869
17DAP/reference	0.96646	0.523
27DAP/reference	0.98698	0.598
39DAP/reference	0.89045	0.152
41DAP/reference	0.89662	0.212
42DAP/reference	0.80759	0.073
43DAP/reference	0.81298	0.042
47DAP/reference	0.75816	0.026
52DAP/reference	0.95499	0.38
57DAP/reference	0.96103	0.384

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.99713	0.699
17DAP/reference	0.99239	0.727
27DAP/reference	0.945	0.337
39DAP/reference	1.022	0.813
41DAP/reference	0.91465	0.371
42DAP/reference	0.99157	0.816
43DAP/reference	0.989	0.66
47DAP/reference	0.95427	0.434
52DAP/reference	0.93724	0.573
57DAP/reference	1.02296	1

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.05454	1
26DAP/20DAP	0.93277	1
34DAP/26DAP	1.47459	0.542
51DAP/34DAP	2.17067
52DAP/51DAP	1.03733	0.86
53DAP/52DAP	0.99034	0.882
55DAP/53DAP	1.06557	0.645
57DAP/55DAP	0.93854	0.59
62DAP/57DAP	0.81649
68DAP/62DAP	1.62879	0.316
68DAP/14DAP	1.11323	0.739

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.14713	0.782

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.54521
Mature Green Tomato/Ripe Tomato	1.77028	0.119
Immature Eggplant/Mature Eggplant	1.58829	0.05
Ripe Pepper/Ripe Tomato	1.02206
Mature Eggplant/Ripe Tomato	1.33854

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	1.04846	1
12-2/M82	N/A	N/A
12-4/M82	0.85101
1-3/M82	N/A	N/A
2-1-1/M82	N/A	N/A
2-1/M82	N/A	N/A
2-6/M82	1.08007	1
3-2/M82	1.1138	0.967
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	N/A	N/A
5-3/M82	0.91907	1
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	0.83846	0.881
9-3-2/M82	2.00432

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.07211	1
IL2-6/WTpooled	1.16977	0.531
IL7-5/WTpooled	0.68585	1
IL7-3/WTpooled	1.02105	1
IL12-4/WTpooled	0.86221	0.581
IL1-4/WTpooled	1.06275	1
WT/WTpooled	1.00146	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	1.00571	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.95081	1
DC3000/delta hrp 6h	1.06408	1
DC3000/delta hrp 12h	0.94712	1
DC3000/delta hrp 24h	0.91201	0.473

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	0.81287	1
Exp 36h	1.17934	0.693
Exp 60h	0.99968	1

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

hybridization	ratio	FDR (corrected p value)
self-self	0.9925	1
Var 0h	1.23751	0.936
Var 12h I row2-row1	0.94754	0.627
Var 12h NI row2-row1	0.89395	0.546
Var 36h I row2-row1	1.85812	1
Var 36h NI row2-row1	3.96269	1
Var 60h I row2-row1	1.45999	0.271
Var 60h NI row2-row1	1.02691	1
Time course 0hI-0hNI	0.94115	0.43
Time course 12hI-12hNI	0.97304	0.847
Time course 36hI-36hNI	0.7565	0.023
Time course 60hI-60hNI	0.25824	0.006

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)	1.16289	0.212
transgenic ySAMdc/azygous control (breaker)	0.99958	1
transgenic ySAMdc/azygous control (red)	0.98812	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.99945	0.94

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.97242	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.99288	1
Manapal/WT (break)	1.34339	0.183
Manapal/WT (red)	1.35927	0.413