Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.4.3.14

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	2.01086	0.033
27DAP/17DAP	1.0511	0.92
39DAP/27DAP	0.82036	0.286
41DAP/39DAP	0.79671	0.235
42DAP/41DAP	1.24908	0.913
43DAP/42DAP	0.92769	0.813
47DAP/43DAP	1.13067	0.68
52DAP/47DAP	1.06736	0.883
57DAP/52DAP	1.376	0.904

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.81351	0.031
17DAP/reference	0.83278	0.194
27DAP/reference	0.94849	0.538
39DAP/reference	1.13294	0.114
41DAP/reference	0.8285	0.008
42DAP/reference	0.92316	0.078
43DAP/reference	0.92347
47DAP/reference	1.02729	1
52DAP/reference	1.33717	0.096
57DAP/reference	N/A	N/A

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.21379	0.144
27DAP/17DAP	0.93256	0.748
39DAP/27DAP	0.91259	0.616
41DAP/39DAP	0.91987	0.822
42DAP/41DAP	1.57196	0.009
43DAP/42DAP	0.7465	0.044
47DAP/43DAP	0.78244	0.272
52DAP/47DAP	4.27381	0.046
57DAP/52DAP	4.08954	0.05
57DAP/7DAP	7.94898	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.17457	0.185
17DAP/reference	1.50919	0.012
27DAP/reference	1.60874	0.008
39DAP/reference	1.32525	0.077
41DAP/reference	1.08766	0.812
42DAP/reference	1.4964	0.018
43DAP/reference	1.39735	0.05
47DAP/reference	1.17838	0.292
52DAP/reference	1.39714	0.055
57DAP/reference	1.28036	0.049

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.93604	0.441
17DAP/reference	0.78835	0.019
27DAP/reference	0.96488	0.467
39DAP/reference	1.15453	0.449
41DAP/reference	0.9786	0.481
42DAP/reference	0.94106	0.289
43DAP/reference	0.72823	0.012
47DAP/reference	0.83954	0.06
52DAP/reference	0.96726	0.302
57DAP/reference	0.66672	0.003

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.34115	0.067
17DAP/reference	1.06465	0.956
27DAP/reference	1.57563	0.056
39DAP/reference	1.34284	0.045
41DAP/reference	1.28972	0.024
42DAP/reference	1.26509	0.08
43DAP/reference	1.45774	0.053
47DAP/reference	0.9486	0.357
52DAP/reference	1.58701	0.155
57DAP/reference	1.37622	0.016

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.92306	1
26DAP/20DAP	2.57193	1
34DAP/26DAP	5.5554	0.542
51DAP/34DAP	1.80579	0.038
52DAP/51DAP	4.10163	0.035
53DAP/52DAP	0.71638
55DAP/53DAP	1.20575	0.131
57DAP/55DAP	0.31426	0.018
62DAP/57DAP	1.29223	0.35
68DAP/62DAP	1.22285	1
68DAP/14DAP	1.38865	0.087

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.15879	0.021

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	2.051
Mature Green Tomato/Ripe Tomato	1.20425	0.237
Immature Eggplant/Mature Eggplant	0.69718	0.292
Ripe Pepper/Ripe Tomato	0.21168	0.224
Mature Eggplant/Ripe Tomato	0.6046	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	N/A	N/A
12-2/M82	N/A	N/A
12-4/M82	N/A	N/A
1-3/M82	N/A	N/A
2-1-1/M82	N/A	N/A
2-1/M82	N/A	N/A
2-6/M82	N/A	N/A
3-2/M82	N/A	N/A
4-1-1/M82	N/A	N/A
4-1/M82	N/A	N/A
4-3-2/M82	N/A	N/A
4-3/M82	N/A	N/A
5-3/M82	N/A	N/A
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	N/A	N/A
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.95506	1
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	0.37702
IL1-4/WTpooled	1.18446	1
WT/WTpooled	1.02471	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	1.11954	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.91966	1
DC3000/delta hrp 6h	0.95633	0.95
DC3000/delta hrp 12h	1.09902	1
DC3000/delta hrp 24h	0.60029	0.034

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.37013
DC3000 delta B/DC3000 delta AB	1.18911	0.243

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	N/A	N/A
Exp 36h	0.93662	0.82
Exp 60h	0.92913	0.664

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

hybridization	ratio	FDR (corrected p value)
self-self	1.04192	1
Var 0h	1.07572	1
Var 12h I row2-row1	0.84189	0.705
Var 12h NI row2-row1	1.25448	0.649
Var 36h I row2-row1	1.19168	1
Var 36h NI row2-row1	1.82027	0.482
Var 60h I row2-row1	0.77516	0.374
Var 60h NI row2-row1	1.08214	1
Time course 0hI-0hNI	0.88607	0.472
Time course 12hI-12hNI	1.06263	1
Time course 36hI-36hNI	0.84778	0.19
Time course 60hI-60hNI	0.59565	0.006

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)	1.08085	0.397
transgenic ySAMdc/azygous control (breaker)	1.08038	1
transgenic ySAMdc/azygous control (red)	1.04463	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.93285	0.043

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.12823	0.239

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.76795	1
Manapal/WT (break)	0.73477	0.333
Manapal/WT (red)	1.62729	0.413