Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.3.20.19

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.07588	0.798
27DAP/17DAP	1.0633	0.88
39DAP/27DAP	1.11444	0.692
41DAP/39DAP	0.97864	0.893
42DAP/41DAP	1.05293	1
43DAP/42DAP	1.06553	1
47DAP/43DAP	1.16804	0.474
52DAP/47DAP	0.92166	0.742
57DAP/52DAP	0.98255	0.971

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.85572	0.058
17DAP/reference	1.00956	0.764
27DAP/reference	0.99273	0.779
39DAP/reference	0.95149	0.554
41DAP/reference	0.89369	0.267
42DAP/reference	0.95508	0.176
43DAP/reference	1.02377	0.705
47DAP/reference	0.95987	0.174
52DAP/reference	0.8834	0.108
57DAP/reference	0.9295	0.199

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.89056	0.036
27DAP/17DAP	1.14187	0.541
39DAP/27DAP	0.85599	0.167
41DAP/39DAP	1.15239	0.837
42DAP/41DAP	0.99095	0.84
43DAP/42DAP	0.77326	0.027
47DAP/43DAP	0.93639	0.734
52DAP/47DAP	1.33403	0.29
57DAP/52DAP	1.35103	0.32
57DAP/7DAP	1.3265	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.06745	0.664
17DAP/reference	1.322	0.054
27DAP/reference	1.61292	0.013
39DAP/reference	1.67991	0.006
41DAP/reference	1.24376	0.086
42DAP/reference	1.22304	0.013
43DAP/reference	1.16357	0.056
47DAP/reference	1.17526	0.124
52DAP/reference	1.1497	0.308
57DAP/reference	1.61995	0.011

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.83391	0.053
17DAP/reference	0.78682	0.01
27DAP/reference	0.92059	0.304
39DAP/reference	0.93786	0.208
41DAP/reference	0.90264	0.064
42DAP/reference	0.86247	0.05
43DAP/reference	0.96091	0.361
47DAP/reference	0.86549	0.022
52DAP/reference	0.87802	0.011
57DAP/reference	0.79728	0.058

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.98327	0.607
17DAP/reference	0.94805	0.462
27DAP/reference	1.2812	0.025
39DAP/reference	1.22298	0.03
41DAP/reference	1.04322	0.521
42DAP/reference	1.14596	0.15
43DAP/reference	0.97782	0.614
47DAP/reference	1.0021	0.687
52DAP/reference	1.04067	0.979
57DAP/reference	1.14206	0.214

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.92901	1
26DAP/20DAP	2.20876	0.098
34DAP/26DAP	1.83633	0.106
51DAP/34DAP	2.11838
52DAP/51DAP	1.10628	1
53DAP/52DAP	0.69918	0.186
55DAP/53DAP	0.87296	0.163
57DAP/55DAP	0.85618	0.556
62DAP/57DAP	0.99675	1
68DAP/62DAP	1.13345	0.722
68DAP/14DAP	1.17059	0.453

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	4.39262	0.014

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.96959	0.089
Mature Green Tomato/Ripe Tomato	2.95406	0.032
Immature Eggplant/Mature Eggplant	0.7975	0.077
Ripe Pepper/Ripe Tomato	0.64881	0.224
Mature Eggplant/Ripe Tomato	1.03643	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.03284	1
1-1-2/M82	0.88519	1
12-2/M82	N/A	N/A
12-4/M82	0.83105
1-3/M82	2.07536	0.479
2-1-1/M82	0.9088	0.465
2-1/M82	N/A	N/A
2-6/M82	1.22425
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	1.22988	1
5-3/M82	0.98401	1
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	1.57128	0.324
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.52522
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	1.23054
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	1.23487	0.785
IL1-4/WTpooled	0.68964	0.415
WT/WTpooled	1.01537	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	1.1069	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.94533	0.807
DC3000/delta hrp 6h	0.94196	0.95
DC3000/delta hrp 12h	1.0528	1
DC3000/delta hrp 24h	1.01796	1

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.84902
DC3000 delta B/DC3000 delta AB	1.39054	0.217

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.1165	1
Exp 36h	1.27767	0.693
Exp 60h	1.59468	0.237

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

hybridization	ratio	FDR (corrected p value)
self-self	1.03649	1
Var 0h	N/A	N/A
Var 12h I row2-row1	1.09178	0.613
Var 12h NI row2-row1	0.9306	0.906
Var 36h I row2-row1	1.38318	1
Var 36h NI row2-row1	1.64862	1
Var 60h I row2-row1	1.00579	0.562
Var 60h NI row2-row1	1.07495	1
Time course 0hI-0hNI	1.02617	0.867
Time course 12hI-12hNI	1.05	0.777
Time course 36hI-36hNI	1.05666	0.722
Time course 60hI-60hNI	1.39423	0.009

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)	0.96785	0.348
transgenic ySAMdc/azygous control (breaker)	0.84939	0.251
transgenic ySAMdc/azygous control (red)	0.88756	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.0103	0.495

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.90333	0.308

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.78573	1
Manapal/WT (break)	0.82789	0.333
Manapal/WT (red)	2.75072	0.222