Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.3.4.19

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.74326	0.206
27DAP/17DAP	0.95207	0.945
39DAP/27DAP	1.0859	0.965
41DAP/39DAP	0.74778	0.15
42DAP/41DAP	1.14648	0.825
43DAP/42DAP	1.00772	0.937
47DAP/43DAP	1.50563	0.222
52DAP/47DAP	1.64402	0.438
57DAP/52DAP	0.84573	0.748

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.87023	0.211
17DAP/reference	0.61409	0.008
27DAP/reference	0.79906	0.028
39DAP/reference	0.52264	0.009
41DAP/reference	0.51579	0.009
42DAP/reference	0.85679	0.188
43DAP/reference	0.65005	0.129
47DAP/reference	0.7988	0.174
52DAP/reference	1.27563	0.032
57DAP/reference	1.38174

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.10369	0.508
27DAP/17DAP	0.65688	0.137
39DAP/27DAP	1.33972	0.06
41DAP/39DAP	1.13325	1
42DAP/41DAP	0.80155	0.022
43DAP/42DAP	1.04754	0.627
47DAP/43DAP	1.06602	0.601
52DAP/47DAP	1.76265	0.048
57DAP/52DAP	2.13555	0.03
57DAP/7DAP	1.36137	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.41332	0.041
17DAP/reference	0.94119	0.253
27DAP/reference	0.85829	0.02
39DAP/reference	1.17958	0.101
41DAP/reference	1.09331	0.28
42DAP/reference	1.10189	0.132
43DAP/reference	1.46764	0.012
47DAP/reference	1.0923	0.292
52DAP/reference	0.9977	0.679
57DAP/reference	1.36516	0.031

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.82826	0.257
17DAP/reference	0.77968	0.072
27DAP/reference	0.87416	0.282
39DAP/reference	0.94174	0.526
41DAP/reference	1.19212	0.45
42DAP/reference	1.21149	0.072
43DAP/reference	0.65408	0.032
47DAP/reference	0.99891	0.73
52DAP/reference	0.81069	0.04
57DAP/reference	0.47691	0.03

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.28404	0.18
17DAP/reference	0.69316	0.121
27DAP/reference	0.87892	0.155
39DAP/reference	0.87067	0.092
41DAP/reference	0.72058	0.023
42DAP/reference	0.89022	0.287
43DAP/reference	0.88883	0.179
47DAP/reference	0.82458	0.103
52DAP/reference	1.24193	0.13
57DAP/reference	1.32098	0.026

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.59901	0.786
26DAP/20DAP	1.21133	0.905
34DAP/26DAP	0.71226	0.165
51DAP/34DAP	2.00113	0.103
52DAP/51DAP	0.78453	1
53DAP/52DAP	1.30251	0.24
55DAP/53DAP	0.83734	0.072
57DAP/55DAP	0.91066	0.652
62DAP/57DAP	1.12581	0.8
68DAP/62DAP	1.08341	0.956
68DAP/14DAP	2.05138	0.153

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	2.01937	0.014

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.6849	0.179
Mature Green Tomato/Ripe Tomato	0.34793	0.017
Immature Eggplant/Mature Eggplant	1.65105	0.05
Ripe Pepper/Ripe Tomato	0.54652	0.224
Mature Eggplant/Ripe Tomato	0.30586	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.0936	1
1-1-2/M82	1.32048	0.75
12-2/M82	0.93862	0.955
12-4/M82	0.74312	0.319
1-3/M82	1.79518	0.479
2-1-1/M82	1.10257	1
2-1/M82	N/A	N/A
2-6/M82	1.08077	0.594
3-2/M82	1.20568
4-1-1/M82	1.12074	1
4-1/M82	1.17273	1
4-3-2/M82	0.91048
4-3/M82	1.22032
5-3/M82	0.90729	1
6-2/M82	0.99717	1
6-3/M82	1.22859	1
7-1/M82	0.94876
7-2/M82	0.92876	1
9-3-2/M82	1.1921	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.72997	0.247
IL2-6/WTpooled	1.01499	1
IL7-5/WTpooled	0.68501	1
IL7-3/WTpooled	1.06698	1
IL12-4/WTpooled	0.80205	0.581
IL1-4/WTpooled	0.91784	0.457
WT/WTpooled	1.07771	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	1.08868	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.04345	0.914
DC3000/delta hrp 6h	1.17442	0.609
DC3000/delta hrp 12h	1.24619	1
DC3000/delta hrp 24h	0.97986	0.91

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.43958	0.229
DC3000 delta B/DC3000 delta AB	1.52037	0.093

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.8935	1
Exp 36h	1.47936	0.693
Exp 60h	1.49948	0.563

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

hybridization	ratio	FDR (corrected p value)
self-self	1.01439	1
Var 0h	N/A	N/A
Var 12h I row2-row1	N/A	N/A
Var 12h NI row2-row1	N/A	N/A
Var 36h I row2-row1	0.95505	1
Var 36h NI row2-row1	N/A	N/A
Var 60h I row2-row1	N/A	N/A
Var 60h NI row2-row1	N/A	N/A
Time course 0hI-0hNI	1.02417	0.867
Time course 12hI-12hNI	0.97189	0.831
Time course 36hI-36hNI	0.90638	0.035
Time course 60hI-60hNI	1.16669	0.029

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)	1.06283	0.482
transgenic ySAMdc/azygous control (breaker)	0.58637	0.131
transgenic ySAMdc/azygous control (red)	0.91755	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.47232	0.055

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.51681	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.92377	1
Manapal/WT (break)	0.96461	1
Manapal/WT (red)	0.98117	0.863