Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.1.3.5

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.02976	0.904
27DAP/17DAP	1.22812	0.804
39DAP/27DAP	1.02124	1
41DAP/39DAP	1.12799	0.597
42DAP/41DAP	1.55965	0.162
43DAP/42DAP	0.9947	0.937
47DAP/43DAP	0.8006	0.407
52DAP/47DAP	1.18049	0.773
57DAP/52DAP	1.0561	0.962

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.08863	0.46
17DAP/reference	1.21905	0.061
27DAP/reference	1.07418	0.672
39DAP/reference	1.06761	0.256
41DAP/reference	1.3376	0.012
42DAP/reference	1.3454	0.001
43DAP/reference	1.05801	0.758
47DAP/reference	1.23825	0.005
52DAP/reference	1.32954	0.011
57DAP/reference	N/A	N/A

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.99954	1
27DAP/17DAP	1.03959	0.863
39DAP/27DAP	1.10488	0.236
41DAP/39DAP	0.79272	0.022
42DAP/41DAP	1.09138	0.593
43DAP/42DAP	1.12214	0.052
47DAP/43DAP	1.02603	0.857
52DAP/47DAP	1.06972	0.71
57DAP/52DAP	0.88459	0.199
57DAP/7DAP	1.37605	0.153

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.92564	0.495
17DAP/reference	0.93229	0.018
27DAP/reference	0.87152	0.01
39DAP/reference	0.89791	0.011
41DAP/reference	0.95932	0.394
42DAP/reference	1.01321	0.686
43DAP/reference	0.85915	0.01
47DAP/reference	0.99597	1
52DAP/reference	0.86714	0.016
57DAP/reference	0.93366	0.132

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.99219	0.884
17DAP/reference	1.09575	0.151
27DAP/reference	1.23315	0.107
39DAP/reference	1.16855	0.355
41DAP/reference	1.27063	0.018
42DAP/reference	1.20424	0.027
43DAP/reference	1.07732	0.509
47DAP/reference	1.22344	0.009
52DAP/reference	1.15667	0.02
57DAP/reference	1.16078	0.046

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.98533	0.699
17DAP/reference	1.0691	0.612
27DAP/reference	0.93265	0.092
39DAP/reference	0.97357	0.591
41DAP/reference	0.92147	0.096
42DAP/reference	1.23068	0.279
43DAP/reference	1.16134	0.209
47DAP/reference	1.24115	0.017
52DAP/reference	0.89172	0.247
57DAP/reference	1.42889	0.083

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.01809	1
26DAP/20DAP	0.94366	0.317
34DAP/26DAP	0.94353	0.619
51DAP/34DAP	0.87763	0.112
52DAP/51DAP	0.99444	1
53DAP/52DAP	1.0267	0.868
55DAP/53DAP	0.98707	0.876
57DAP/55DAP	1.07499	0.854
62DAP/57DAP	1.24325	0.018
68DAP/62DAP	0.91772	0.543
68DAP/14DAP	0.95324	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.28202	0.02

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.93439	0.591
Mature Green Tomato/Ripe Tomato	0.57503	0.132
Immature Eggplant/Mature Eggplant	2.15486	0.05
Ripe Pepper/Ripe Tomato	0.2091	0.224
Mature Eggplant/Ripe Tomato	0.51315	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.18347	0.591
1-1-2/M82	1.07905	1
12-2/M82	1.05795	1
12-4/M82	1.06392	1
1-3/M82	1.03725	1
2-1-1/M82	0.87712	0.683
2-1/M82	0.85969	0.74
2-6/M82	0.99612	1
3-2/M82	1.13596	0.84
4-1-1/M82	0.94693	1
4-1/M82	1.01654	1
4-3-2/M82	0.80351	1
4-3/M82	1.04565	1
5-3/M82	1.05135	1
6-2/M82	1.0785
6-3/M82	0.91656	1
7-1/M82	0.99642
7-2/M82	0.70668	0.527
9-3-2/M82	0.73951

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.73739	0.247
IL2-6/WTpooled	0.96157	1
IL7-5/WTpooled	0.61212	1
IL7-3/WTpooled	0.87178	0.418
IL12-4/WTpooled	1.0163	1
IL1-4/WTpooled	0.96435	1
WT/WTpooled	1.12222	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	0.96787	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.94794	1
DC3000/delta hrp 6h	0.87486	0.95
DC3000/delta hrp 12h	1.12726	1
DC3000/delta hrp 24h	0.94462	0.564

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.95513	0.765
DC3000 delta B/DC3000 delta AB	0.8939	0.456

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.88124	0.328
Exp 36h	1.09219	1
Exp 60h	1.43663	0.227

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

hybridization	ratio	FDR (corrected p value)
self-self	N/A	N/A
Var 0h	0.75972	1
Var 12h I row2-row1	0.78177	0.627
Var 12h NI row2-row1	0.86898	0.488
Var 36h I row2-row1	0.81281	0.805
Var 36h NI row2-row1	1.2321	0.482
Var 60h I row2-row1	0.95748
Var 60h NI row2-row1	1.12116	1
Time course 0hI-0hNI	0.832
Time course 12hI-12hNI	0.8363
Time course 36hI-36hNI	N/A	N/A
Time course 60hI-60hNI	N/A	N/A

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)	1.03625	0.541
transgenic ySAMdc/azygous control (breaker)	0.88036	0.15
transgenic ySAMdc/azygous control (red)	1.78492	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.06673	0.092

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.16087	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.30772	0.084
Manapal/WT (break)	1.03143	1
Manapal/WT (red)	0.90571	0.36