Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.1.2.20

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.99391	0.839
27DAP/17DAP	1.06003	1
39DAP/27DAP	1.7515	0.089
41DAP/39DAP	0.89014	0.499
42DAP/41DAP	0.97209	1
43DAP/42DAP	0.95398	0.877
47DAP/43DAP	0.88439	0.595
52DAP/47DAP	1.1826	0.842
57DAP/52DAP	1.18904	0.941

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.16797	0.154
17DAP/reference	1.02156	0.907
27DAP/reference	0.98368	0.683
39DAP/reference	0.98306	0.797
41DAP/reference	1.10933	0.338
42DAP/reference	1.00631	0.731
43DAP/reference	0.98191	0.728
47DAP/reference	1.07648	0.306
52DAP/reference	1.37204	0.043
57DAP/reference	1.13135	0.084

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.18956	0.348
27DAP/17DAP	1.09616	0.73
39DAP/27DAP	0.94972	0.673
41DAP/39DAP	1.01394	1
42DAP/41DAP	0.97555	0.781
43DAP/42DAP	0.78096	0.116
47DAP/43DAP	0.94541	0.656
52DAP/47DAP	1.10569	0.666
57DAP/52DAP	1.52157	0.105
57DAP/7DAP	0.66544	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.00028	1
17DAP/reference	0.91402	0.072
27DAP/reference	0.98495	0.462
39DAP/reference	0.98351	0.552
41DAP/reference	1.0077	1
42DAP/reference	0.80896	0.019
43DAP/reference	0.72966	0.018
47DAP/reference	1.22221	0.279
52DAP/reference	0.84734	0.019
57DAP/reference	0.83555	0.013

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.00904	0.915
17DAP/reference	0.9936	0.766
27DAP/reference	1.215	0.171
39DAP/reference	1.37627	0.068
41DAP/reference	1.26337	0.293
42DAP/reference	1.07111	1
43DAP/reference	1.0416	0.919
47DAP/reference	0.9298	0.261
52DAP/reference	1.15863	0.046
57DAP/reference	1.01726	1

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.00925	1
17DAP/reference	0.97284	0.624
27DAP/reference	0.95545	0.319
39DAP/reference	0.88079	0.058
41DAP/reference	0.89242	0.086
42DAP/reference	1.06527	0.923
43DAP/reference	1.12221	0.565
47DAP/reference	1.08815	0.228
52DAP/reference	0.90552	0.342
57DAP/reference	1.52254	0.132

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.08456	0.966
26DAP/20DAP	2.04413	0.262
34DAP/26DAP	1.34436	1
51DAP/34DAP	1.19923	0.898
52DAP/51DAP	2.15763	0.035
53DAP/52DAP	0.88765	0.307
55DAP/53DAP	1.33784	0.244
57DAP/55DAP	0.69471	0.094
62DAP/57DAP	1.27132	0.002
68DAP/62DAP	1.0393	1
68DAP/14DAP	1.66915	0.063

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.62324	0.02

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.6679	0.17
Mature Green Tomato/Ripe Tomato	1.06595	0.69
Immature Eggplant/Mature Eggplant	1.33631	0.05
Ripe Pepper/Ripe Tomato	1.25377	1
Mature Eggplant/Ripe Tomato	1.25693	0.373

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.97992	0.961
1-1-2/M82	0.99557	1
12-2/M82	1.13591	1
12-4/M82	0.95238	1
1-3/M82	1.10646	1
2-1-1/M82	0.96111	1
2-1/M82	1.1326	1
2-6/M82	1.00402	1
3-2/M82	1.52204
4-1-1/M82	0.94031	1
4-1/M82	0.91585
4-3-2/M82	0.97206
4-3/M82	1.34372	0.268
5-3/M82	1.04589	1
6-2/M82	N/A	N/A
6-3/M82	0.9327	0.857
7-1/M82	N/A	N/A
7-2/M82	1.20464	0.385
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.45783	0.243
IL2-6/WTpooled	0.57232	0.348
IL7-5/WTpooled	0.29579	1
IL7-3/WTpooled	0.46781	0.31
IL12-4/WTpooled	0.67286	0.71
IL1-4/WTpooled	0.67214	0.562
WT/WTpooled	1.06211	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	0.91694	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.05221	0.921
DC3000/delta hrp 6h	0.94712	0.95
DC3000/delta hrp 12h	1.36804	1
DC3000/delta hrp 24h	1.07628	0.582

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.12899	0.183
DC3000 delta B/DC3000 delta AB	1.11491	0.386

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.89901	1
Exp 36h	1.76901	0.489
Exp 60h	1.46868	0.563

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

hybridization	ratio	FDR (corrected p value)
self-self	0.93946	1
Var 0h	0.7949	0.933
Var 12h I row2-row1	1.00702	1
Var 12h NI row2-row1	1.25771	0.34
Var 36h I row2-row1	1.16494	0.368
Var 36h NI row2-row1	1.05201	1
Var 60h I row2-row1	0.97911	1
Var 60h NI row2-row1	0.92995	1
Time course 0hI-0hNI	0.9441	0.623
Time course 12hI-12hNI	1.00142	1
Time course 36hI-36hNI	1.1799	0.063
Time course 60hI-60hNI	0.97114	0.646

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)	1.08612	0.541
transgenic ySAMdc/azygous control (breaker)	1.02542	1
transgenic ySAMdc/azygous control (red)	1.15112	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.09105	0.135

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.85053	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.93127	1
Manapal/WT (break)	1.06283	1
Manapal/WT (red)	1.11542	1