Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.3.10.7

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.89827	0.065
27DAP/17DAP	1.16939	0.842
39DAP/27DAP	1.34266	0.42
41DAP/39DAP	0.74709	0.182
42DAP/41DAP	1.08675	0.938
43DAP/42DAP	1.00746	0.937
47DAP/43DAP	0.87199	0.591
52DAP/47DAP	0.7479	0.339
57DAP/52DAP	1.10839	0.969

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.81962	0.026
17DAP/reference	0.88792	0.012
27DAP/reference	0.92436	0.286
39DAP/reference	0.94588	0.391
41DAP/reference	0.88485	0.012
42DAP/reference	0.82379	0.002
43DAP/reference	0.97794	0.708
47DAP/reference	0.88583	0.019
52DAP/reference	0.91	0.195
57DAP/reference	1.03012	0.511

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	2.37114	0.041
27DAP/17DAP	1.13668	0.576
39DAP/27DAP	0.94521	0.712
41DAP/39DAP	0.98027	0.875
42DAP/41DAP	1.15913	0.675
43DAP/42DAP	0.83796	0.07
47DAP/43DAP	1.00122	0.983
52DAP/47DAP	1.13494	0.776
57DAP/52DAP	1.26454	0.389
57DAP/7DAP	1.97206	0.365

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.0952	0.368
17DAP/reference	1.086	0.18
27DAP/reference	0.93544	0.375
39DAP/reference	1.2415	0.282
41DAP/reference	1.08545	0.745
42DAP/reference	1.07257	0.889
43DAP/reference	1.40388	0.178
47DAP/reference	1.06331	0.837
52DAP/reference	0.92477	0.213
57DAP/reference	1.16256	0.268

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.95829	0.623
17DAP/reference	0.90889	0.326
27DAP/reference	0.87012	0.119
39DAP/reference	0.90886	0.147
41DAP/reference	0.98101	0.472
42DAP/reference	0.96975	0.433
43DAP/reference	1.2245	0.308
47DAP/reference	0.94711	0.149
52DAP/reference	0.96314	0.433
57DAP/reference	0.86215	0.073

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.95615	0.489
17DAP/reference	0.9761	0.647
27DAP/reference	1.03071	0.805
39DAP/reference	1.06514	0.437
41DAP/reference	0.92796	0.371
42DAP/reference	1.11011	0.55
43DAP/reference	0.93754	0.384
47DAP/reference	1.02385	1
52DAP/reference	0.86088	0.216
57DAP/reference	0.98979	0.682

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.06754	0.966
26DAP/20DAP	1.57998	0.176
34DAP/26DAP	1.07375	1
51DAP/34DAP	0.85484	0.472
52DAP/51DAP	0.67686	0.151
53DAP/52DAP	1.25247	0.055
55DAP/53DAP	0.79935	0.14
57DAP/55DAP	1.19786	0.71
62DAP/57DAP	0.64427	0.002
68DAP/62DAP	1.25399	0.813
68DAP/14DAP	1.37646	0.036

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	2.53106	0.052

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	1.17462	0.881
Immature Eggplant/Mature Eggplant	0.40005	0.062
Ripe Pepper/Ripe Tomato	N/A	N/A
Mature Eggplant/Ripe Tomato	5.03205	0.268

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	1.33473	1
12-2/M82	N/A	N/A
12-4/M82	1.26796	1
1-3/M82	0.83616
2-1-1/M82	N/A	N/A
2-1/M82	N/A	N/A
2-6/M82	1.13643
3-2/M82	N/A	N/A
4-1-1/M82	N/A	N/A
4-1/M82	1.05425
4-3-2/M82	1.02319
4-3/M82	N/A	N/A
5-3/M82	0.71821	0.49
6-2/M82	N/A	N/A
6-3/M82	0.5952
7-1/M82	1.38654
7-2/M82	N/A	N/A
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	1.20253	0.531
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.90216	0.31
IL12-4/WTpooled	1.10415	0.695
IL1-4/WTpooled	1.0641	1
WT/WTpooled	1.05527	0.805

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	1.07166	0.479

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.09253	0.894
DC3000/delta hrp 6h	N/A	N/A
DC3000/delta hrp 12h	0.3234
DC3000/delta hrp 24h	1.05493	0.595

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.42867	0.042
DC3000 delta B/DC3000 delta AB	1.09387	0.472

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	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
self-self	0.97948	1
Var 0h	0.60529	0.782
Var 12h I row2-row1	1.09205	0.544
Var 12h NI row2-row1	0.91956	0.546
Var 36h I row2-row1	1.08252	0.489
Var 36h NI row2-row1	1.28187	0.276
Var 60h I row2-row1	0.8346	0.374
Var 60h NI row2-row1	0.93042	1
Time course 0hI-0hNI	1.06594	0.662
Time course 12hI-12hNI	0.95015	0.526
Time course 36hI-36hNI	0.90316	0.099
Time course 60hI-60hNI	0.90721	0.047

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)	2.35478	0.331
transgenic ySAMdc/azygous control (breaker)	1.08104	1
transgenic ySAMdc/azygous control (red)	1.98489	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.00878	0.619

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.37452	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.61175	1
Manapal/WT (break)	1.08124	1
Manapal/WT (red)	0.85474	0.607