Tomato Functional Genomics Database (TFGD)

Expression of 1-1-4.2.8.12

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.13606	0.77
27DAP/17DAP	1.22521	0.793
39DAP/27DAP	2.29578	0.03
41DAP/39DAP	0.75286	0.171
42DAP/41DAP	2.06865	0.026
43DAP/42DAP	2.16221	0.03
47DAP/43DAP	0.48761	0.049
52DAP/47DAP	1.39991	0.525
57DAP/52DAP	0.92819	0.932

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.93093	0.284
17DAP/reference	1.20463	0.041
27DAP/reference	1.07628	0.375
39DAP/reference	1.09549	0.57
41DAP/reference	1.30335	0.02
42DAP/reference	0.87781	0.004
43DAP/reference	1.01036	0.928
47DAP/reference	0.87261	0.003
52DAP/reference	0.7826	0.042
57DAP/reference	0.86797	0.086

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	3.16548	0.06
27DAP/17DAP	0.54869	0.091
39DAP/27DAP	2.30349	0.057
41DAP/39DAP	0.85217	0.434
42DAP/41DAP	1.33861	0.425
43DAP/42DAP	4.08184	0.013
47DAP/43DAP	0.76425	0.042
52DAP/47DAP	0.62374	0.037
57DAP/52DAP	1.19185	0.402
57DAP/7DAP	3.0236	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.5485	0.076
17DAP/reference	0.44428	0.011
27DAP/reference	0.73887	0.012
39DAP/reference	1.30307	0.157
41DAP/reference	0.90622	0.341
42DAP/reference	3.6535	0.012
43DAP/reference	4.40582	0.006
47DAP/reference	2.03094	0.139
52DAP/reference	1.12382	0.428
57DAP/reference	0.93757	0.341

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.90824	0.475
17DAP/reference	1.36473	0.009
27DAP/reference	1.11179	0.745
39DAP/reference	1.83541	0.011
41DAP/reference	1.09901	0.502
42DAP/reference	1.16684	0.398
43DAP/reference	1.33211	0.149
47DAP/reference	1.64429	0.009
52DAP/reference	1.75401	0.006
57DAP/reference	1.37034	0.007

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.56788	0.057
17DAP/reference	1.12322	0.537
27DAP/reference	0.6122	0.043
39DAP/reference	0.89272	0.246
41DAP/reference	0.77174	0.058
42DAP/reference	2.13851	0.015
43DAP/reference	2.00769	0.071
47DAP/reference	0.83879	0.006
52DAP/reference	2.05712	0.106
57DAP/reference	0.80897	0.074

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.88014	0.787
26DAP/20DAP	1.40585	0.118
34DAP/26DAP	0.82262	0.381
51DAP/34DAP	1.19435	0.473
52DAP/51DAP	1.06778	0.808
53DAP/52DAP	0.94005	0.732
55DAP/53DAP	1.02484	0.908
57DAP/55DAP	1.27004	0.906
62DAP/57DAP	1.1535	0.723
68DAP/62DAP	0.84717	0.263
68DAP/14DAP	1.28094	0.521

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	18.446	0.014

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	4.99138	0.058
Mature Green Tomato/Ripe Tomato	0.26452	0.03
Immature Eggplant/Mature Eggplant	0.30435	0.062
Ripe Pepper/Ripe Tomato	1.06665	0.258
Mature Eggplant/Ripe Tomato	1.86409	0.373

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	N/A	N/A
12-2/M82	N/A	N/A
12-4/M82	2.67793
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	N/A	N/A
3-2/M82	N/A	N/A
4-1-1/M82	N/A	N/A
4-1/M82	N/A	N/A
4-3-2/M82	1.42091	0.241
4-3/M82	N/A	N/A
5-3/M82	0.86145
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	0.6527
7-2/M82	N/A	N/A
9-3-2/M82	1.69891	0.196

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.08412
IL2-6/WTpooled	1.74079	0.395
IL7-5/WTpooled	0.87372
IL7-3/WTpooled	0.62531	0.294
IL12-4/WTpooled	0.89519	0.566
IL1-4/WTpooled	1.1792	0.426
WT/WTpooled	0.93172	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	0.83299	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	N/A	N/A
DC3000/delta hrp 6h	0.96695	0.95
DC3000/delta hrp 12h	1.14237	1
DC3000/delta hrp 24h	1.15212	0.453

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.09215	0.598
DC3000 delta B/DC3000 delta AB	0.97923	0.916

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.7699	0.328
Exp 36h	0.67835	0.449
Exp 60h	0.57353	0.266

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

hybridization	ratio	FDR (corrected p value)
self-self	0.95347	1
Var 0h	0.27893	0.202
Var 12h I row2-row1	0.98877	0.418
Var 12h NI row2-row1	0.96709	0.82
Var 36h I row2-row1	0.8316	1
Var 36h NI row2-row1	1.00578	1
Var 60h I row2-row1	1.09058	0.562
Var 60h NI row2-row1	0.94987	0.458
Time course 0hI-0hNI	1.00451	1
Time course 12hI-12hNI	0.90059	0.089
Time course 36hI-36hNI	0.95691	0.26
Time course 60hI-60hNI	0.75375	0.006

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)	1.00031	1
transgenic ySAMdc/azygous control (breaker)	0.70347	0.15
transgenic ySAMdc/azygous control (red)	1.19289	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.00912	0.525

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.67875	0.255

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.62978	0.096
Manapal/WT (break)	0.64831	0.333
Manapal/WT (red)	1.15584	0.413