Tomato Functional Genomics Database (TFGD)

Expression of 1-1-4.1.4.16

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.96436	0.743
27DAP/17DAP	1.19824	0.849
39DAP/27DAP	1.07266	1
41DAP/39DAP	1.02472	0.994
42DAP/41DAP	1.1389	0.755
43DAP/42DAP	1.12812	0.867
47DAP/43DAP	0.97313	0.821
52DAP/47DAP	0.92741	0.752
57DAP/52DAP	1.11148	0.969

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.01778	1
17DAP/reference	0.82426	0.025
27DAP/reference	0.9378	0.304
39DAP/reference	1.07693	0.734
41DAP/reference	0.83727	0.026
42DAP/reference	1.10202	0.219
43DAP/reference	1.07338	0.163
47DAP/reference	1.16948	0.002
52DAP/reference	1.16805	0.048
57DAP/reference	1.18483	0.025

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.34805	0.058
27DAP/17DAP	0.88076	0.418
39DAP/27DAP	1.33467	0.064
41DAP/39DAP	0.96894	0.945
42DAP/41DAP	1.26767	0.055
43DAP/42DAP	1.23232	0.04
47DAP/43DAP	0.91272	0.525
52DAP/47DAP	0.95097	0.801
57DAP/52DAP	1.03754	0.871
57DAP/7DAP	1.66903	0.23

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.27155	0.072
17DAP/reference	1.24913	0.01
27DAP/reference	1.47507	0.012
39DAP/reference	1.6539	0.005
41DAP/reference	1.55268	0.012
42DAP/reference	1.6322	0.006
43DAP/reference	1.66186	0.006
47DAP/reference	1.77746	0.014
52DAP/reference	1.78092	0.007
57DAP/reference	1.75142	0.004

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.94055	0.592
17DAP/reference	1.10829	0.264
27DAP/reference	1.41701	0.028
39DAP/reference	1.19365	0.059
41DAP/reference	1.37569	0.042
42DAP/reference	1.21946	0.051
43DAP/reference	0.93588	0.414
47DAP/reference	1.2044	0.027
52DAP/reference	1.79848	0.168
57DAP/reference	1.0032	0.789

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.19761	0.076
17DAP/reference	1.01852	0.932
27DAP/reference	1.07358	0.312
39DAP/reference	1.41386	0.007
41DAP/reference	1.30782	0.02
42DAP/reference	1.64411	0.009
43DAP/reference	1.47891	0.029
47DAP/reference	1.35955	0.007
52DAP/reference	1.79489	0.032
57DAP/reference	1.75284	0.019

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.22264	0.966
26DAP/20DAP	1.1249	0.855
34DAP/26DAP	0.92573	0.841
51DAP/34DAP	1.22616	0.445
52DAP/51DAP	0.81417	0.151
53DAP/52DAP	0.87512	0.455
55DAP/53DAP	0.88202	0.313
57DAP/55DAP	1.59714	0.51
62DAP/57DAP	1.05648	1
68DAP/62DAP	1.19237	0.533
68DAP/14DAP	1.29457	0.071

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.63172	0.015

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.59031	0.124
Mature Green Tomato/Ripe Tomato	1.22632	0.267
Immature Eggplant/Mature Eggplant	0.90302	0.105
Ripe Pepper/Ripe Tomato	1.09744	0.258
Mature Eggplant/Ripe Tomato	0.66619	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.97421	0.961
1-1-2/M82	1.13639	1
12-2/M82	0.8203	0.678
12-4/M82	0.9462	1
1-3/M82	1.97208	0.248
2-1-1/M82	0.5393
2-1/M82	0.6464	0.322
2-6/M82	1.16432	0.505
3-2/M82	1.01705
4-1-1/M82	1.08219	1
4-1/M82	1.03176	1
4-3-2/M82	1.47087	0.241
4-3/M82	1.28795	1
5-3/M82	1.09726	1
6-2/M82	1.29172	0.198
6-3/M82	1.03724	1
7-1/M82	1.13227	0.598
7-2/M82	1.37708	0.324
9-3-2/M82	1.57981	0.196

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.27062	0.212
IL2-6/WTpooled	1.0013	1
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.8267	0.418
IL12-4/WTpooled	1.07239	0.695
IL1-4/WTpooled	1.03859	1
WT/WTpooled	1.03225	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	1.04147	0.309

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.81278
DC3000/delta hrp 6h	0.98186	0.95
DC3000/delta hrp 12h	1.07263	1
DC3000/delta hrp 24h	1.15863	0.243

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	N/A	N/A
DC3000 delta B/DC3000 delta AB	1.30531

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	N/A	N/A
Exp 36h	0.91812	0.879
Exp 60h	0.77941	0.664

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

hybridization	ratio	FDR (corrected p value)
self-self	N/A	N/A
Var 0h	1.03932	0.305
Var 12h I row2-row1	N/A	N/A
Var 12h NI row2-row1	N/A	N/A
Var 36h I row2-row1	N/A	N/A
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	N/A	N/A
Time course 12hI-12hNI	N/A	N/A
Time course 36hI-36hNI	N/A	N/A
Time course 60hI-60hNI	N/A	N/A

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)	0.89482	0.338
transgenic ySAMdc/azygous control (breaker)	1.22282	0.178
transgenic ySAMdc/azygous control (red)	1.12113	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.10278	0.261

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.83491	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.14967	0.307
Manapal/WT (break)	0.93835	1
Manapal/WT (red)	1.01853	1