Tomato Functional Genomics Database (TFGD)

Expression of 1-1-6.1.14.16

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.71623	0.114
27DAP/17DAP	0.87995	0.665
39DAP/27DAP	1.52431	0.102
41DAP/39DAP	0.58378	0.045
42DAP/41DAP	0.84179	1
43DAP/42DAP	1.08651	1
47DAP/43DAP	0.54212	0.057
52DAP/47DAP	1.26515	0.608
57DAP/52DAP	1.20507	0.737

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.5831	0.033
17DAP/reference	1.05039	0.737
27DAP/reference	0.62983	0.012
39DAP/reference	0.65721	0.042
41DAP/reference	0.71604	0.013
42DAP/reference	1.08769	0.13
43DAP/reference	0.78092	0.027
47DAP/reference	0.79199	0.007
52DAP/reference	0.55638	0.014
57DAP/reference	0.72572	0.011

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.81851	0.064
27DAP/17DAP	1.06513	0.771
39DAP/27DAP	0.795	0.04
41DAP/39DAP	1.15254	1
42DAP/41DAP	1.0412	0.991
43DAP/42DAP	0.86113	0.048
47DAP/43DAP	0.99885	0.997
52DAP/47DAP	0.60108	0.049
57DAP/52DAP	0.847	0.445
57DAP/7DAP	0.36166	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	2.89238	0.024
17DAP/reference	2.0937	0.006
27DAP/reference	1.41925	0.01
39DAP/reference	1.25032	0.018
41DAP/reference	1.44815	0.012
42DAP/reference	1.30723	0.132
43DAP/reference	1.23428	0.066
47DAP/reference	1.13656	0.304
52DAP/reference	1.27349	0.086
57DAP/reference	1.0398	0.851

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.25584	0.404
17DAP/reference	1.53981	0.01
27DAP/reference	1.31409	0.095
39DAP/reference	0.94848	0.33
41DAP/reference	1.33066	0.011
42DAP/reference	1.35053	0.023
43DAP/reference	0.85004	0.181
47DAP/reference	1.05758	0.589
52DAP/reference	0.62072	0.004
57DAP/reference	0.56454	0.002

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	2.15005	0.016
17DAP/reference	1.61177	0.197
27DAP/reference	1.49518	0.031
39DAP/reference	1.60694	0.007
41DAP/reference	1.11117	0.062
42DAP/reference	1.28677	0.045
43DAP/reference	1.20531	0.205
47DAP/reference	0.5285	0.005
52DAP/reference	0.92213	0.385
57DAP/reference	0.85216	0.134

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.08626	0.966
26DAP/20DAP	3.44393	0.098
34DAP/26DAP	0.78632	0.412
51DAP/34DAP	1.06269	0.581
52DAP/51DAP	0.98065	1
53DAP/52DAP	0.80138	0.148
55DAP/53DAP	0.87463	0.163
57DAP/55DAP	0.96363	0.799
62DAP/57DAP	0.93809	0.871
68DAP/62DAP	0.82852	0.314
68DAP/14DAP	1.15256	0.594

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	3.97464	0.014

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.96963	0.726
Mature Green Tomato/Ripe Tomato	1.7302	0.017
Immature Eggplant/Mature Eggplant	0.9827	0.912
Ripe Pepper/Ripe Tomato	1.37759	1
Mature Eggplant/Ripe Tomato	1.43995	0.268

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.94175	0.944
1-1-2/M82	1.27173	1
12-2/M82	0.88063	0.955
12-4/M82	1.10489	1
1-3/M82	1.71203	0.479
2-1-1/M82	1.07414	1
2-1/M82	0.92932	1
2-6/M82	1.26083	0.452
3-2/M82	1.16485
4-1-1/M82	1.50727	1
4-1/M82	1.23098	1
4-3-2/M82	1.90653
4-3/M82	1.44851	0.268
5-3/M82	1.29652	0.496
6-2/M82	2.33626	0.253
6-3/M82	1.04412	1
7-1/M82	1.11977	1
7-2/M82	1.62823	0.318
9-3-2/M82	1.54177	1

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	0.98697
IL1-4/WTpooled	N/A	N/A
WT/WTpooled	0.80248

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	1.27918	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.00954	0.921
DC3000/delta hrp 6h	0.97005	0.95
DC3000/delta hrp 12h	1.21571	1
DC3000/delta hrp 24h	1.13103	0.243

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.24399	0.049
DC3000 delta B/DC3000 delta AB	1.54703	0.081

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.2657	1
Exp 36h	1.13372	1
Exp 60h	1.37817	0.237

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

hybridization	ratio	FDR (corrected p value)
self-self	0.99828	1
Var 0h	0.45671	0.933
Var 12h I row2-row1	0.86103	0.39
Var 12h NI row2-row1	1.11023	0.649
Var 36h I row2-row1	1.15622	0.908
Var 36h NI row2-row1	0.89455	0.61
Var 60h I row2-row1	0.84139	0.285
Var 60h NI row2-row1	0.84326	0.756
Time course 0hI-0hNI	1.12927	0.486
Time course 12hI-12hNI	1.0096	0.885
Time course 36hI-36hNI	1.37332	0.005
Time course 60hI-60hNI	1.83176	0.008

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)	1.06345	0.699
transgenic ySAMdc/azygous control (breaker)	1.02322	1
transgenic ySAMdc/azygous control (red)	1.18421	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.27817	0.213

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.95726	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.12504	0.14
Manapal/WT (break)	1.12657	0.183
Manapal/WT (red)	0.93296	0.36