Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.3.10.13

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	2.67274	0.067
27DAP/17DAP	1.01863	1
39DAP/27DAP	2.01119	0.03
41DAP/39DAP	0.64504	0.08
42DAP/41DAP	0.97835	1
43DAP/42DAP	0.83107	0.754
47DAP/43DAP	0.50859	0.049
52DAP/47DAP	0.96468	0.832
57DAP/52DAP	0.89812	0.82

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.34123	0.018
17DAP/reference	1.01304	0.813
27DAP/reference	0.93818	0.137
39DAP/reference	0.92566	0.234
41DAP/reference	1.22903	0.062
42DAP/reference	1.00256	0.645
43DAP/reference	0.85872	0.084
47DAP/reference	0.89301	0.023
52DAP/reference	0.85556	0.223
57DAP/reference	0.95645	0.294

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.9378	0.496
27DAP/17DAP	1.53284	0.026
39DAP/27DAP	1.00998	0.862
41DAP/39DAP	2.27488	0.03
42DAP/41DAP	0.88408	0.362
43DAP/42DAP	0.41155	0.019
47DAP/43DAP	1.47189	0.013
52DAP/47DAP	0.64512	0.103
57DAP/52DAP	0.9523	0.641
57DAP/7DAP	0.69798	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.90537	0.27
17DAP/reference	0.8741	0.044
27DAP/reference	0.92788	0.109
39DAP/reference	0.76986	0.011
41DAP/reference	0.85646	0.111
42DAP/reference	0.74308	0.01
43DAP/reference	0.75591	0.025
47DAP/reference	1.35744	0.324
52DAP/reference	0.72317	0.031
57DAP/reference	0.73558	0.009

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.11868	0.463
17DAP/reference	1.48815	0.013
27DAP/reference	1.22442	0.798
39DAP/reference	1.61597	0.011
41DAP/reference	1.77467	0.053
42DAP/reference	1.32843	0.05
43DAP/reference	1.57087	0.079
47DAP/reference	1.42162	0.036
52DAP/reference	1.41541	0.006
57DAP/reference	1.59337	0.016

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.01361	0.804
17DAP/reference	1.46327	0.269
27DAP/reference	0.82182	0.042
39DAP/reference	0.97684	0.504
41DAP/reference	0.9433	0.331
42DAP/reference	0.89131	0.02
43DAP/reference	0.82214	0.041
47DAP/reference	0.62077	0.004
52DAP/reference	0.69227	0.061
57DAP/reference	0.80102	0.043

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.91228	0.981
26DAP/20DAP	0.89964	0.512
34DAP/26DAP	1.06874	1
51DAP/34DAP	1.13769	0.666
52DAP/51DAP	0.80967	1
53DAP/52DAP	0.87652	0.393
55DAP/53DAP	1.05914	0.994
57DAP/55DAP	1.2861	0.091
62DAP/57DAP	0.91159	0.681
68DAP/62DAP	0.96132	0.81
68DAP/14DAP	0.89869	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	4.16354	0.014

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	27.9794	0.089
Mature Green Tomato/Ripe Tomato	4.37328	0.077
Immature Eggplant/Mature Eggplant	0.8793	0.159
Ripe Pepper/Ripe Tomato	0.31367	0.293
Mature Eggplant/Ripe Tomato	0.67663	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.86104	0.536
1-1-2/M82	1.02607
12-2/M82	1.68259
12-4/M82	1.1787
1-3/M82	1.05615	1
2-1-1/M82	N/A	N/A
2-1/M82	N/A	N/A
2-6/M82	1.14668	0.594
3-2/M82	N/A	N/A
4-1-1/M82	0.93677	1
4-1/M82	1.37518
4-3-2/M82	1.60088
4-3/M82	N/A	N/A
5-3/M82	1.9182	0.496
6-2/M82	1.62099
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	0.97068	1
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.07271	1
IL2-6/WTpooled	0.99229	1
IL7-5/WTpooled	1.2384	0.792
IL7-3/WTpooled	1.18954	1
IL12-4/WTpooled	0.97125	0.71
IL1-4/WTpooled	1.12184	0.426
WT/WTpooled	0.93131	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	1.18912	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.99871	1
DC3000/delta hrp 6h	1.0121	0.95
DC3000/delta hrp 12h	1.34715	1
DC3000/delta hrp 24h	1.01868	0.797

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.28463	0.046
DC3000 delta B/DC3000 delta AB	1.57747	0.079

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.24715	1
Exp 36h	1.56984	0.693
Exp 60h	1.98793	0.399

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

hybridization	ratio	FDR (corrected p value)
self-self	0.97829	1
Var 0h	1.61091	0.782
Var 12h I row2-row1	0.85241	0.467
Var 12h NI row2-row1	1.53702	0.34
Var 36h I row2-row1	1.14199	1
Var 36h NI row2-row1	0.66476	0.522
Var 60h I row2-row1	0.83409	0.439
Var 60h NI row2-row1	0.66582	0.335
Time course 0hI-0hNI	1.25182	0.297
Time course 12hI-12hNI	1.14239	0.475
Time course 36hI-36hNI	3.21454	0.004
Time course 60hI-60hNI	7.17176	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)	1.10696	0.455
transgenic ySAMdc/azygous control (breaker)	1.16056	0.248
transgenic ySAMdc/azygous control (red)	1.11693	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.95777	0.343

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.93395	0.284

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	3.55034	0.09
Manapal/WT (break)	1.22155	0.381
Manapal/WT (red)	0.6472	0.424