Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.4.20.13

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.94345	0.683
27DAP/17DAP	0.94315	0.918
39DAP/27DAP	0.8669	0.482
41DAP/39DAP	1.45544	0.293
42DAP/41DAP	1.06052	0.941
43DAP/42DAP	0.94977	0.807
47DAP/43DAP	0.99982	0.943
52DAP/47DAP	1.08494	0.869
57DAP/52DAP	0.95948	0.936

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.90946	0.087
17DAP/reference	1.0265	0.764
27DAP/reference	1.02718	0.468
39DAP/reference	0.88272	0.024
41DAP/reference	0.88528	0.201
42DAP/reference	0.88619	0.005
43DAP/reference	0.98226	0.728
47DAP/reference	0.90067	0.025
52DAP/reference	0.92907	0.275
57DAP/reference	0.99452	0.701

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.35262	0.23
27DAP/17DAP	1.41756	0.279
39DAP/27DAP	0.92712	0.579
41DAP/39DAP	1.02176	1
42DAP/41DAP	1.06409	1
43DAP/42DAP	1.20161	0.664
47DAP/43DAP	1.00704	0.971
52DAP/47DAP	0.9573	0.884
57DAP/52DAP	1.08971	1
57DAP/7DAP	1.46598	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.98934	0.682
17DAP/reference	0.82036	0.072
27DAP/reference	0.79561	0.026
39DAP/reference	0.66366	0.015
41DAP/reference	0.81859	0.064
42DAP/reference	0.6994	0.042
43DAP/reference	0.65895	0.019
47DAP/reference	0.85686	0.168
52DAP/reference	0.795	0.049
57DAP/reference	0.87286	0.132

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.98648	0.756
17DAP/reference	0.86891	0.063
27DAP/reference	0.84694	0.053
39DAP/reference	0.84255	0.055
41DAP/reference	0.9254	0.169
42DAP/reference	0.76564	0.012
43DAP/reference	0.92986	0.328
47DAP/reference	0.87887	0.035
52DAP/reference	0.8832	0.008
57DAP/reference	0.92089	0.226

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.895	0.214
17DAP/reference	0.83303	0.109
27DAP/reference	0.89603	0.206
39DAP/reference	0.85878	0.063
41DAP/reference	0.85442	0.148
42DAP/reference	0.87531	0.134
43DAP/reference	0.85753	0.061
47DAP/reference	0.88282	0.04
52DAP/reference	0.78581	0.197
57DAP/reference	0.86039	0.187

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.06855	0.966
26DAP/20DAP	1.41697	0.598
34DAP/26DAP	1.04591	1
51DAP/34DAP	1.29185	0.111
52DAP/51DAP	1.14909	0.565
53DAP/52DAP	0.87351	0.435
55DAP/53DAP	1.10302	0.826
57DAP/55DAP	1.02544	0.997
62DAP/57DAP	1.00047	1
68DAP/62DAP	1.11098	0.936
68DAP/14DAP	1.19668	0.153

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.57099	0.028

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.6943	0.26
Mature Green Tomato/Ripe Tomato	0.98538	0.715
Immature Eggplant/Mature Eggplant	1.17181	0.123
Ripe Pepper/Ripe Tomato	1.97302	0.244
Mature Eggplant/Ripe Tomato	1.86313	0.373

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.01707
1-1-2/M82	0.66132
12-2/M82	N/A	N/A
12-4/M82	0.89524	0.298
1-3/M82	N/A	N/A
2-1-1/M82	N/A	N/A
2-1/M82	1.02217
2-6/M82	1.13681	0.425
3-2/M82	0.9228	1
4-1-1/M82	N/A	N/A
4-1/M82	0.84419
4-3-2/M82	0.87922
4-3/M82	1.0161
5-3/M82	0.87317	0.642
6-2/M82	1.31709
6-3/M82	0.93044	1
7-1/M82	1.09801
7-2/M82	N/A	N/A
9-3-2/M82	0.98808

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	N/A	N/A
IL1-4/WTpooled	N/A	N/A
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	0.80665	0.341

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.09791	0.921
DC3000/delta hrp 6h	0.99497	0.95
DC3000/delta hrp 12h	1.13555	1
DC3000/delta hrp 24h	1.48696	0.043

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.62891
DC3000 delta B/DC3000 delta AB	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.95475	1
Exp 36h	1.09941	1
Exp 60h	1.27242	0.399

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

hybridization	ratio	FDR (corrected p value)
self-self	1.05508	1
Var 0h	N/A	N/A
Var 12h I row2-row1	1.10995	0.406
Var 12h NI row2-row1	1.13247	1
Var 36h I row2-row1	1.2645	0.601
Var 36h NI row2-row1	0.68482	0.469
Var 60h I row2-row1	0.83205	0.285
Var 60h NI row2-row1	1.19929	1
Time course 0hI-0hNI	1.1093	0.603
Time course 12hI-12hNI	1.09366	0.293
Time course 36hI-36hNI	0.97779	0.524
Time course 60hI-60hNI	1.38923	0.08

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)	0.97487	0.3
transgenic ySAMdc/azygous control (breaker)	0.76866	0.142
transgenic ySAMdc/azygous control (red)	0.92139	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.93903	0.071

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.1642	0.277

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.91853	1
Manapal/WT (break)	0.7643	0.299
Manapal/WT (red)	1.55245	0.413