Tomato Functional Genomics Database (TFGD)

Expression of 1-1-4.4.6.16

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.65171	0.032
27DAP/17DAP	0.85907	0.644
39DAP/27DAP	1.71125	0.04
41DAP/39DAP	0.93918	0.568
42DAP/41DAP	0.56156	0.397
43DAP/42DAP	0.77864	0.346
47DAP/43DAP	0.46265	0.049
52DAP/47DAP	1.57333	0.268
57DAP/52DAP	1.08969	0.977

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.9194	0.262
17DAP/reference	1.00235	1
27DAP/reference	1.08288	0.384
39DAP/reference	1.24323	0.016
41DAP/reference	1.16138	0.016
42DAP/reference	1.12226	0.015
43DAP/reference	1.1479	0.069
47DAP/reference	1.17915	0.015
52DAP/reference	1.01557	1
57DAP/reference	1.08661	0.186

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.30688	0.023
27DAP/17DAP	2.03946	0.031
39DAP/27DAP	0.41016	0.029
41DAP/39DAP	1.29396	0.656
42DAP/41DAP	1.06599	1
43DAP/42DAP	1.86894	0.014
47DAP/43DAP	1.04202	0.956
52DAP/47DAP	0.69563	0.183
57DAP/52DAP	1.51941	0.063
57DAP/7DAP	0.49628	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	2.32343	0.03
17DAP/reference	1.28594	0.297
27DAP/reference	1.32953	0.088
39DAP/reference	1.2957	0.069
41DAP/reference	1.51468	0.046
42DAP/reference	1.44109	0.016
43DAP/reference	1.34098	0.027
47DAP/reference	1.20573	0.139
52DAP/reference	1.24394	0.13
57DAP/reference	1.0855	0.41

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.87864	0.17
17DAP/reference	0.84161	0.023
27DAP/reference	0.99254	0.663
39DAP/reference	0.99121	0.586
41DAP/reference	0.88561	0.177
42DAP/reference	1.04926	0.81
43DAP/reference	1.07475	0.751
47DAP/reference	0.98487	0.59
52DAP/reference	1.12614	0.029
57DAP/reference	0.96668	0.488

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.75593	0.018
17DAP/reference	1.10971	0.865
27DAP/reference	1.29726	0.039
39DAP/reference	1.16383	0.038
41DAP/reference	1.13663	0.181
42DAP/reference	1.31106	0.251
43DAP/reference	1.25682	0.028
47DAP/reference	1.34475	0.009
52DAP/reference	1.04393	1
57DAP/reference	1.02852	0.771

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.0438	0.966
26DAP/20DAP	2.3444	0.097
34DAP/26DAP	0.80959	0.387
51DAP/34DAP	0.95048	0.703
52DAP/51DAP	0.95089	1
53DAP/52DAP	0.96078	0.715
55DAP/53DAP	0.8525	0.041
57DAP/55DAP	2.9673	0.085
62DAP/57DAP	1.06089	0.935
68DAP/62DAP	1.41261	0.051
68DAP/14DAP	1.33109	0.084

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.26115	0.077

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	1.29764	0.095
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	0.51837	1
Mature Eggplant/Ripe Tomato	0.95481	0.373

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.03097	0.877
1-1-2/M82	0.93764
12-2/M82	0.75509
12-4/M82	1.3085
1-3/M82	2.3063
2-1-1/M82	0.94708
2-1/M82	N/A	N/A
2-6/M82	1.20573
3-2/M82	1.39167	0.549
4-1-1/M82	0.97218
4-1/M82	N/A	N/A
4-3-2/M82	N/A	N/A
4-3/M82	1.23569	1
5-3/M82	0.6912
6-2/M82	4.48601
6-3/M82	1.08444
7-1/M82	2.57066
7-2/M82	1.43837
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.00753
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	0.83521
IL1-4/WTpooled	1.23909
WT/WTpooled	0.80734

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	1.05906	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.98789	1
DC3000/delta hrp 6h	N/A	N/A
DC3000/delta hrp 12h	2.04144
DC3000/delta hrp 24h	1.83597	0.035

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.86299	0.027
DC3000 delta B/DC3000 delta AB	0.75445	0.045

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

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

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

hybridization	ratio	FDR (corrected p value)
self-self	1.00276	1
Var 0h	1.68012	1
Var 12h I row2-row1	1.25039	0.613
Var 12h NI row2-row1	1.13867	0.649
Var 36h I row2-row1	0.81297	0.805
Var 36h NI row2-row1	1.25473	1
Var 60h I row2-row1	0.63261	0.582
Var 60h NI row2-row1	1.10381	0.904
Time course 0hI-0hNI	0.97878	0.922
Time course 12hI-12hNI	0.94845	0.687
Time course 36hI-36hNI	0.83969	0.057
Time course 60hI-60hNI	0.69007	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)	0.73317	0.229
transgenic ySAMdc/azygous control (breaker)	0.97314	1
transgenic ySAMdc/azygous control (red)	0.75959	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.10145	0.042

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.98471	1
Manapal/WT (break)	0.8751	1
Manapal/WT (red)	0.75243	0.242