Tomato Functional Genomics Database (TFGD)

Expression of 1-1-8.3.10.21

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.47924	0.018
27DAP/17DAP	0.59302	0.071
39DAP/27DAP	0.99502	0.641
41DAP/39DAP	0.41338	0.041
42DAP/41DAP	0.90363	1
43DAP/42DAP	1.46707	0.277
47DAP/43DAP	0.9626	0.847
52DAP/47DAP	0.64058	0.246
57DAP/52DAP	0.92253	0.92

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	2.22737	0.006
17DAP/reference	1.45624	0.021
27DAP/reference	1.72529	0.025
39DAP/reference	0.75882	0.047
41DAP/reference	0.55464	0.009
42DAP/reference	0.77581	0.005
43DAP/reference	0.70574	0.058
47DAP/reference	0.65909	0.002
52DAP/reference	0.65705	0.035
57DAP/reference	0.85906	0.031

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.30924	0.026
27DAP/17DAP	1.87502	0.098
39DAP/27DAP	0.47092	0.039
41DAP/39DAP	0.38255	0.013
42DAP/41DAP	1.31041	0.487
43DAP/42DAP	1.77464	0.017
47DAP/43DAP	0.6135	0.016
52DAP/47DAP	0.85976	0.753
57DAP/52DAP	0.73056	0.382
57DAP/7DAP	0.08293	0.219

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	2.37982	0.024
17DAP/reference	1.15822	0.297
27DAP/reference	0.90441	0.031
39DAP/reference	0.67476	0.011
41DAP/reference	0.72197	0.015
42DAP/reference	0.73527	0.1
43DAP/reference	0.5254	0.009
47DAP/reference	0.52166	0.04
52DAP/reference	0.50596	0.012
57DAP/reference	0.54051	0.005

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.08125	0.903
17DAP/reference	1.06734	0.824
27DAP/reference	0.97105	0.519
39DAP/reference	0.64135	0.024
41DAP/reference	0.73309	0.01
42DAP/reference	0.86881	0.121
43DAP/reference	0.43632	0.002
47DAP/reference	0.57854	0.009
52DAP/reference	0.54189	0.004
57DAP/reference	0.44764	0.002

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	3.46542	0.015
17DAP/reference	1.99433	0.035
27DAP/reference	1.70396	0.034
39DAP/reference	0.8089	0.076
41DAP/reference	0.81022	0.077
42DAP/reference	0.74136	0.087
43DAP/reference	0.67159	0.098
47DAP/reference	0.71062	0.02
52DAP/reference	0.38144	0.047
57DAP/reference	0.79842	0.083

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.24468	0.966
26DAP/20DAP	0.91794	1
34DAP/26DAP	0.9544	0.945
51DAP/34DAP	0.52108	0.06
52DAP/51DAP	1.12334	0.662
53DAP/52DAP	0.25509
55DAP/53DAP	0.31544	0.016
57DAP/55DAP	0.53846	0.031
62DAP/57DAP	1.5264	0.081
68DAP/62DAP	2.51512	0.259
68DAP/14DAP	0.84759	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.08951	0.019

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	2.40976	0.058
Mature Green Tomato/Ripe Tomato	15.4864	0.015
Immature Eggplant/Mature Eggplant	0.36391	0.063
Ripe Pepper/Ripe Tomato	33.4529	0.233
Mature Eggplant/Ripe Tomato	36.5533	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.37074
1-1-2/M82	1.02716	1
12-2/M82	0.99521	1
12-4/M82	0.96168	1
1-3/M82	N/A	N/A
2-1-1/M82	1.68949
2-1/M82	N/A	N/A
2-6/M82	0.96508
3-2/M82	N/A	N/A
4-1-1/M82	0.87407
4-1/M82	N/A	N/A
4-3-2/M82	N/A	N/A
4-3/M82	1.45861
5-3/M82	1.04279	1
6-2/M82	N/A	N/A
6-3/M82	1.44781
7-1/M82	0.61449
7-2/M82	0.89375
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	0.99571	1
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.27922	1
IL12-4/WTpooled	1.13446	0.557
IL1-4/WTpooled	1.07109
WT/WTpooled	1.06053	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	0.94344	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.96564	1
DC3000/delta hrp 6h	1.01196	1
DC3000/delta hrp 12h	1.22081	1
DC3000/delta hrp 24h	0.65811	0.198

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.55081	0.057
DC3000 delta B/DC3000 delta AB	0.50835	0.022

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.97824	1
Exp 36h	0.70962	0.504
Exp 60h	0.71848	0.259

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

hybridization	ratio	FDR (corrected p value)
self-self	0.99499	1
Var 0h	1.15833	0.936
Var 12h I row2-row1	0.87021	0.565
Var 12h NI row2-row1	0.85708	0.546
Var 36h I row2-row1	0.93871	0.575
Var 36h NI row2-row1	1.10263	1
Var 60h I row2-row1	1.01725	1
Var 60h NI row2-row1	1.12508	0.904
Time course 0hI-0hNI	1.06628	0.799
Time course 12hI-12hNI	0.92544	0.431
Time course 36hI-36hNI	0.80557	0.043
Time course 60hI-60hNI	0.15499	0.005

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)	0.64647	0.297
transgenic ySAMdc/azygous control (breaker)	2.561	1
transgenic ySAMdc/azygous control (red)	1.00522	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.65387	0.059

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	6.13516	0.229

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.36925	0.14
Manapal/WT (break)	1.26985	1
Manapal/WT (red)	1.04406	1