Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.2.1.21

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.76495	0.249
27DAP/17DAP	1.19929	0.881
39DAP/27DAP	0.85749	0.443
41DAP/39DAP	1.38532	0.31
42DAP/41DAP	0.96907	1
43DAP/42DAP	0.84574	0.514
47DAP/43DAP	1.13014	0.715
52DAP/47DAP	1.56619	0.305
57DAP/52DAP	0.91462	0.852

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.85453	0.326
17DAP/reference	0.95694	0.194
27DAP/reference	0.96364	0.444
39DAP/reference	0.9406	0.149
41DAP/reference	0.97555	0.667
42DAP/reference	1.03901	0.523
43DAP/reference	0.93699	0.118
47DAP/reference	0.98679	0.535
52DAP/reference	1.08482	0.388
57DAP/reference	0.87983	0.054

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.96415	0.663
27DAP/17DAP	0.99828	0.969
39DAP/27DAP	1.01974	0.824
41DAP/39DAP	1.01027	1
42DAP/41DAP	1.07321	0.753
43DAP/42DAP	1.03637	0.664
47DAP/43DAP	1.03168	0.884
52DAP/47DAP	1.01947	0.945
57DAP/52DAP	0.91878	0.494
57DAP/7DAP	1.07708	0.365

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.93509	0.122
17DAP/reference	0.95772	0.253
27DAP/reference	0.89807	0.01
39DAP/reference	0.95137	0.012
41DAP/reference	0.95354	0.174
42DAP/reference	0.9843	0.531
43DAP/reference	0.89278	0.012
47DAP/reference	0.89417	0.101
52DAP/reference	0.88916	0.049
57DAP/reference	0.88139	0.008

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.11247	0.106
17DAP/reference	1.16632	0.022
27DAP/reference	1.15496	0.174
39DAP/reference	1.18147	0.225
41DAP/reference	1.04699	0.893
42DAP/reference	1.07412	0.744
43DAP/reference	1.17131	0.13
47DAP/reference	0.91591	0.105
52DAP/reference	1.05764	0.444
57DAP/reference	1.19002	0.182

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.92764	0.065
17DAP/reference	1.03606	0.898
27DAP/reference	0.90632	0.051
39DAP/reference	0.89594	0.035
41DAP/reference	0.91833	0.024
42DAP/reference	1.00621	1
43DAP/reference	0.99091	0.712
47DAP/reference	0.91427	0.215
52DAP/reference	0.83639	0.109
57DAP/reference	0.86527	0.08

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.94238	0.997
26DAP/20DAP	1.03212	0.962
34DAP/26DAP	0.91623	0.741
51DAP/34DAP	1.0423	0.829
52DAP/51DAP	1.08969	0.431
53DAP/52DAP	0.99473	0.983
55DAP/53DAP	1.00478	0.917
57DAP/55DAP	1.13851	0.906
62DAP/57DAP	0.98476	1
68DAP/62DAP	1.02453	1
68DAP/14DAP	0.95866	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.0826	0.74

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.95152
Mature Green Tomato/Ripe Tomato	0.93895	0.317
Immature Eggplant/Mature Eggplant	0.86999	0.105
Ripe Pepper/Ripe Tomato	1.34612
Mature Eggplant/Ripe Tomato	1.66968

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.02268	1
1-1-2/M82	0.9485	1
12-2/M82	1.05356	1
12-4/M82	0.9989	1
1-3/M82	0.99606	1
2-1-1/M82	1.16969	0.764
2-1/M82	N/A	N/A
2-6/M82	0.95891	1
3-2/M82	0.97294	1
4-1-1/M82	0.89281	1
4-1/M82	0.84308	1
4-3-2/M82	0.92865	1
4-3/M82	0.90249	0.25
5-3/M82	1.03144	1
6-2/M82	0.91532
6-3/M82	0.99738	1
7-1/M82	N/A	N/A
7-2/M82	1.04268	1
9-3-2/M82	0.91199	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.81158	0.243
IL2-6/WTpooled	0.7678	0.383
IL7-5/WTpooled	0.73847	0.559
IL7-3/WTpooled	0.85921	1
IL12-4/WTpooled	1.23408	1
IL1-4/WTpooled	1.04237	1
WT/WTpooled	1.14005	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	0.72661	0.75

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.99313	1
DC3000/delta hrp 6h	1.60658	0.857
DC3000/delta hrp 12h	0.96984	1
DC3000/delta hrp 24h	1.02085	1

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.13247	0.16
DC3000 delta B/DC3000 delta AB	0.99525	1

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.59378	1
Exp 36h	1.50793	0.489
Exp 60h	0.5374	0.259

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

hybridization	ratio	FDR (corrected p value)
self-self	0.98491	1
Var 0h	1.20965	0.936
Var 12h I row2-row1	0.98034	0.948
Var 12h NI row2-row1	0.91238	0.82
Var 36h I row2-row1	1.06963	1
Var 36h NI row2-row1	0.97432	0.852
Var 60h I row2-row1	1.17562	0.562
Var 60h NI row2-row1	1.08409	0.904
Time course 0hI-0hNI	0.90809	0.45
Time course 12hI-12hNI	0.78766	0.154
Time course 36hI-36hNI	0.80603	0.023
Time course 60hI-60hNI	0.4205	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)	1.0274	0.325
transgenic ySAMdc/azygous control (breaker)	1.42158	0.178
transgenic ySAMdc/azygous control (red)	1.15073	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.0295	0.148

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.709	0.237

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.86432	0.09
Manapal/WT (break)	1.66557	0.126
Manapal/WT (red)	1.73523	0.413