Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.3.3.12

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.16723	0.477
27DAP/17DAP	2.07119	0.592
39DAP/27DAP	1.4747	0.236
41DAP/39DAP	0.83698	0.449
42DAP/41DAP	1.79066	0.145
43DAP/42DAP	0.72751	0.551
47DAP/43DAP	1.18262	0.563
52DAP/47DAP	0.88126	0.673
57DAP/52DAP	1.2309	0.89

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.04263	0.814
17DAP/reference	1.09127	0.143
27DAP/reference	1.06922	0.405
39DAP/reference	1.0674	0.286
41DAP/reference	1.19851	0.019
42DAP/reference	1.04434	0.963
43DAP/reference	0.88775	0.594
47DAP/reference	0.96935	0.503
52DAP/reference	0.93914	0.416
57DAP/reference	N/A	N/A

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.67882	0.158
27DAP/17DAP	3.3531
39DAP/27DAP	1.1433	0.824
41DAP/39DAP	1.20069	0.837
42DAP/41DAP	0.96984	0.759
43DAP/42DAP	1.06249	0.746
47DAP/43DAP	1.35373	0.376
52DAP/47DAP	1.13078	0.624
57DAP/52DAP	1.33783	0.225
57DAP/7DAP	1.2915

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.02862	0.894
17DAP/reference	1.43666	0.025
27DAP/reference	1.46694	0.013
39DAP/reference	1.27943	0.009
41DAP/reference	1.17869	0.232
42DAP/reference	1.33419	0.03
43DAP/reference	1.18945	0.056
47DAP/reference	1.05611	0.915
52DAP/reference	1.09763	0.308
57DAP/reference	1.25591	0.008

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.10455	0.477
17DAP/reference	1.15754	0.113
27DAP/reference	1.09127	0.283
39DAP/reference	1.05905	1
41DAP/reference	1.25427	0.188
42DAP/reference	1.11491	0.317
43DAP/reference	0.9538	0.478
47DAP/reference	1.01256	0.994
52DAP/reference	1.10104	0.393
57DAP/reference	1.36081	0.038

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.1764	0.149
17DAP/reference	1.10238	0.612
27DAP/reference	1.37143	0.031
39DAP/reference	1.2757	0.019
41DAP/reference	1.1907	0.129
42DAP/reference	1.13415	0.364
43DAP/reference	1.16911	0.452
47DAP/reference	1.01835	1
52DAP/reference	1.51313	0.066
57DAP/reference	0.92066	0.353

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.69086
26DAP/20DAP	1.01513
34DAP/26DAP	0.30735
51DAP/34DAP	0.8769	0.747
52DAP/51DAP	0.84148	1
53DAP/52DAP	1.33307	0.428
55DAP/53DAP	1.22714	0.244
57DAP/55DAP	0.71688	0.1
62DAP/57DAP	0.88548	0.871
68DAP/62DAP	1.41653	0.225
68DAP/14DAP	1.3256	0.049

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.65054	0.046

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	N/A	N/A
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	0.33404	0.224
Mature Eggplant/Ripe Tomato	1.12525	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.22465
1-1-2/M82	0.95574	1
12-2/M82	N/A	N/A
12-4/M82	1.09589	1
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	0.95242
3-2/M82	N/A	N/A
4-1-1/M82	N/A	N/A
4-1/M82	1.07047
4-3-2/M82	N/A	N/A
4-3/M82	1.22739
5-3/M82	1.01391	1
6-2/M82	1.80449
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	1.16421
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.27534
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	1.38948	1
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	0.99405
IL1-4/WTpooled	1.00669
WT/WTpooled	N/A	N/A

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	1.52311	0.479

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.03694	0.921
DC3000/delta hrp 6h	1.07457	1
DC3000/delta hrp 12h	1.58456	1
DC3000/delta hrp 24h	1.10685	0.438

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	0.39115

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.23873	1
Exp 36h	1.63616	0.349
Exp 60h	1.91474	0.215

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

hybridization	ratio	FDR (corrected p value)
self-self	1.03154
Var 0h	0.95063	1
Var 12h I row2-row1	1.20026	0.296
Var 12h NI row2-row1	2.07652	0.649
Var 36h I row2-row1	1.33841	0.742
Var 36h NI row2-row1	1.38893	1
Var 60h I row2-row1	0.78315	0.285
Var 60h NI row2-row1	0.8416	0.302
Time course 0hI-0hNI	0.97818	0.763
Time course 12hI-12hNI	2.23559	0.005
Time course 36hI-36hNI	2.81984	0.004
Time course 60hI-60hNI	4.89184	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)	1.2293	0.312
transgenic ySAMdc/azygous control (breaker)	0.5473	0.137
transgenic ySAMdc/azygous control (red)	0.98202	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.97938	0.22

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.52138	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.1208	0.096
Manapal/WT (break)	1.11955	1
Manapal/WT (red)	0.86835	0.242