Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.4.19.9

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	2.61988	0.403
27DAP/17DAP	1.53978	0.809
39DAP/27DAP	1.16936	0.681
41DAP/39DAP	1.01513	1
42DAP/41DAP	1.31886	0.863
43DAP/42DAP	0.92456	0.867
47DAP/43DAP	1.11498	0.966
52DAP/47DAP	0.9292	0.702
57DAP/52DAP	1.12506	0.977

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.91983	0.412
17DAP/reference	0.91387	0.419
27DAP/reference	0.94458	0.24
39DAP/reference	1.09913	0.089
41DAP/reference	0.81045	0.014
42DAP/reference	0.97749	0.348
43DAP/reference	0.99475
47DAP/reference	1.0172	1
52DAP/reference	1.1521	0.121
57DAP/reference	2.46943	0.141

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.28696	0.057
27DAP/17DAP	0.94269	0.724
39DAP/27DAP	0.87697	0.106
41DAP/39DAP	1.00761	1
42DAP/41DAP	0.96894	0.721
43DAP/42DAP	0.97512	0.684
47DAP/43DAP	1.08652	0.593
52DAP/47DAP	0.74646	0.254
57DAP/52DAP	1.10743	0.476
57DAP/7DAP	1.21655	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.18306	0.197
17DAP/reference	1.45684	0.022
27DAP/reference	2.4766	0.006
39DAP/reference	3.13311	0.005
41DAP/reference	5.09594	0.009
42DAP/reference	3.85663	0.006
43DAP/reference	3.30506	0.006
47DAP/reference	1.8578	0.07
52DAP/reference	2.82878	0.007
57DAP/reference	3.23701	0.004

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.79366	0.129
17DAP/reference	0.9875	0.659
27DAP/reference	1.10146	0.244
39DAP/reference	1.14059	0.281
41DAP/reference	1.1356	0.327
42DAP/reference	1.10189	0.332
43DAP/reference	1.002	0.801
47DAP/reference	1.03449	0.867
52DAP/reference	1.25307	0.053
57DAP/reference	0.94232	0.298

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.42244	0.032
17DAP/reference	1.04131	0.627
27DAP/reference	1.58281	0.051
39DAP/reference	2.55082	0.01
41DAP/reference	2.01702	0.007
42DAP/reference	2.18838	0.009
43DAP/reference	1.62792	0.01
47DAP/reference	1.02619	0.901
52DAP/reference	0.83556	0.303
57DAP/reference	1.22955	0.209

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.06282	1
26DAP/20DAP	1.51736	0.142
34DAP/26DAP	1.19888	1
51DAP/34DAP	1.14352	0.339
52DAP/51DAP	0.91938	1
53DAP/52DAP	0.97423	0.824
55DAP/53DAP	0.98394	0.838
57DAP/55DAP	1.05068	0.986
62DAP/57DAP	1.13087	0.723
68DAP/62DAP	1.78041	0.1
68DAP/14DAP	1.41582	0.504

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.06853	0.821

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.6562	0.024
Immature Eggplant/Mature Eggplant	0.23277
Ripe Pepper/Ripe Tomato	0.33074	0.293
Mature Eggplant/Ripe Tomato	0.16028	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.66066	0.634
1-1-2/M82	1.19927	1
12-2/M82	1.03767	1
12-4/M82	0.95568	0.33
1-3/M82	0.30822	0.378
2-1-1/M82	0.7619	0.565
2-1/M82	1.08178	1
2-6/M82	1.01344	1
3-2/M82	0.89659	1
4-1-1/M82	1.00272	1
4-1/M82	0.86031
4-3-2/M82	1.0069
4-3/M82	1.06542	1
5-3/M82	0.95665	1
6-2/M82	0.76848	1
6-3/M82	0.9566	1
7-1/M82	1.09492	1
7-2/M82	0.85857	0.578
9-3-2/M82	0.83299

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	0.93886	1
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.6012
IL12-4/WTpooled	1.1403	0.839
IL1-4/WTpooled	0.80679
WT/WTpooled	1.01283	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	0.75797	0.75

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.01005	1
DC3000/delta hrp 6h	1.34452	0.777
DC3000/delta hrp 12h	1.0253	1
DC3000/delta hrp 24h	1.01326	0.84

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.57304	0.062
DC3000 delta B/DC3000 delta AB	0.60344	0.022

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.97802	1
Exp 36h	1.0065	1
Exp 60h	1.28193	0.563

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

hybridization	ratio	FDR (corrected p value)
self-self	1.0251	1
Var 0h	1.06856	0.936
Var 12h I row2-row1	1.06773	0.58
Var 12h NI row2-row1	0.73546	0.438
Var 36h I row2-row1	0.99135	1
Var 36h NI row2-row1	1.30356	1
Var 60h I row2-row1	0.93976	0.952
Var 60h NI row2-row1	1.18248	0.904
Time course 0hI-0hNI	0.80812	0.075
Time course 12hI-12hNI	1.03169	0.867
Time course 36hI-36hNI	0.87507	0.114
Time course 60hI-60hNI	0.33117	0.005

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)	0.94554	0.428
transgenic ySAMdc/azygous control (breaker)	0.83408	0.251
transgenic ySAMdc/azygous control (red)	1.0741	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.95577	0.181

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.0711	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	N/A	N/A
Manapal/WT (break)	N/A	N/A
Manapal/WT (red)	1.3011	1