Tomato Functional Genomics Database (TFGD)

Expression of 1-1-4.4.19.19

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.17264	0.863
27DAP/17DAP	1.21325	0.793
39DAP/27DAP	2.8531	0.029
41DAP/39DAP	1.48228	0.403
42DAP/41DAP	1.01173	1
43DAP/42DAP	1.3315	0.34
47DAP/43DAP	1.44333	0.278
52DAP/47DAP	1.03458	0.908
57DAP/52DAP	2.25256	0.55

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.63055	0.024
17DAP/reference	0.65833	0.007
27DAP/reference	0.69296	0.02
39DAP/reference	1.27365	0.664
41DAP/reference	0.86624	0.114
42DAP/reference	1.36623	0.002
43DAP/reference	1.1628	0.069
47DAP/reference	2.51146	0.001
52DAP/reference	1.60098	0.008
57DAP/reference	1.62726	0.008

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.0202	0.961
27DAP/17DAP	0.96871	0.821
39DAP/27DAP	1.51754	0.107
41DAP/39DAP	0.85791	0.228
42DAP/41DAP	1.03731	0.861
43DAP/42DAP	1.24782	0.014
47DAP/43DAP	1.35007	0.049
52DAP/47DAP	1.02953	0.965
57DAP/52DAP	1.19866	0.594
57DAP/7DAP	1.46128	0.365

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.62783	0.049
17DAP/reference	0.72198	0.011
27DAP/reference	0.96903	0.375
39DAP/reference	0.96646	0.474
41DAP/reference	1.31194	0.023
42DAP/reference	1.35822	0.046
43DAP/reference	1.12159	0.364
47DAP/reference	1.07481	0.685
52DAP/reference	1.51303	0.019
57DAP/reference	2.60993	0.004

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.54883	0.007
17DAP/reference	0.50318	0.003
27DAP/reference	0.78978	0.087
39DAP/reference	0.88361	0.108
41DAP/reference	1.27394	0.03
42DAP/reference	1.24546	0.03
43DAP/reference	1.00134	0.692
47DAP/reference	3.40444	0.008
52DAP/reference	1.289	0.007
57DAP/reference	1.76553	0.012

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.78966	0.049
17DAP/reference	0.80863	0.21
27DAP/reference	1.15432	0.179
39DAP/reference	1.45738	0.012
41DAP/reference	1.28651	0.019
42DAP/reference	1.53972	0.016
43DAP/reference	1.51571	0.014
47DAP/reference	2.24376	0.005
52DAP/reference	3.44329	0.03
57DAP/reference	1.86535	0.037

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.91656	1
26DAP/20DAP	0.9805	1
34DAP/26DAP	1.10215	1
51DAP/34DAP	1.95151	0.025
52DAP/51DAP	0.81984	1
53DAP/52DAP	1.23083	0.413
55DAP/53DAP	0.74774	0.022
57DAP/55DAP	0.87644	0.443
62DAP/57DAP	2.17202	0.018
68DAP/62DAP	1.11399	0.912
68DAP/14DAP	2.83729	0.021

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.8315	0.115

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.05149	0.037
Mature Green Tomato/Ripe Tomato	0.1762	0.017
Immature Eggplant/Mature Eggplant	31.2528	0.05
Ripe Pepper/Ripe Tomato	1.76736	0.258
Mature Eggplant/Ripe Tomato	0.44788	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.82761	0.613
1-1-2/M82	1.39968	1
12-2/M82	1.04475	1
12-4/M82	1.15457	1
1-3/M82	3.74393	0.479
2-1-1/M82	1.00891	1
2-1/M82	0.95136	0.519
2-6/M82	1.39021	0.385
3-2/M82	1.19897	0.463
4-1-1/M82	1.67289
4-1/M82	1.81129	1
4-3-2/M82	1.91064	0.253
4-3/M82	1.14545	1
5-3/M82	0.4175	0.364
6-2/M82	0.55647	0.481
6-3/M82	0.99048	1
7-1/M82	0.96704	1
7-2/M82	2.40912	0.385
9-3-2/M82	2.15292	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.01759	1
IL2-6/WTpooled	1.12779	0.584
IL7-5/WTpooled	1.09182	0.792
IL7-3/WTpooled	0.90262	0.31
IL12-4/WTpooled	1.00477	1
IL1-4/WTpooled	1.10907	1
WT/WTpooled	0.97333	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	1.06686	1

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	0.93528	0.95
DC3000/delta hrp 12h	0.7856	1
DC3000/delta hrp 24h	0.93385	0.598

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.23768	0.313
DC3000 delta B/DC3000 delta AB	1.37303	0.192

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.24537	1
Exp 36h	1.1995	1
Exp 60h	1.13828	1

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

hybridization	ratio	FDR (corrected p value)
self-self	0.98273	1
Var 0h	0.74629	0.782
Var 12h I row2-row1	0.90074	0.705
Var 12h NI row2-row1	1.57207	0.649
Var 36h I row2-row1	1.04532	1
Var 36h NI row2-row1	0.73774	0.584
Var 60h I row2-row1	0.52691	0.285
Var 60h NI row2-row1	0.72537	0.301
Time course 0hI-0hNI	1.04907	0.662
Time course 12hI-12hNI	1.31276	0.175
Time course 36hI-36hNI	2.86066	0.005
Time course 60hI-60hNI	11.368	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)	0.57018	0.314
transgenic ySAMdc/azygous control (breaker)	0.71893	0.142
transgenic ySAMdc/azygous control (red)	1.11635	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.69855	0.059

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.07087	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	6.63579	0.096
Manapal/WT (break)	4.94433	0.183
Manapal/WT (red)	1.30295	0.15