Tomato Functional Genomics Database (TFGD)

Expression of 1-1-8.3.10.12

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.03069	0.919
27DAP/17DAP	0.67451	0.111
39DAP/27DAP	1.39933	0.215
41DAP/39DAP	0.98842	0.944
42DAP/41DAP	1.20971	0.825
43DAP/42DAP	1.17829	0.957
47DAP/43DAP	1.02384	0.884
52DAP/47DAP	0.82503	0.589
57DAP/52DAP	1.12193	0.96

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.68492	0.035
17DAP/reference	0.53595	0.008
27DAP/reference	0.76438	0.089
39DAP/reference	0.635	0.027
41DAP/reference	0.37555	0.009
42DAP/reference	0.787	0.028
43DAP/reference	0.80772	0.036
47DAP/reference	0.85482	0.065
52DAP/reference	1.41357	0.096
57DAP/reference	1.37858	0.013

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.55821	0.04
27DAP/17DAP	0.78645	0.195
39DAP/27DAP	0.68052	0.045
41DAP/39DAP	1.27519	0.417
42DAP/41DAP	1.04188	0.947
43DAP/42DAP	0.7191	0.022
47DAP/43DAP	1.07264	0.963
52DAP/47DAP	1.0534	0.868
57DAP/52DAP	1.32194	0.213
57DAP/7DAP	0.6585	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.82803	0.071
17DAP/reference	0.81516	0.011
27DAP/reference	0.80481	0.019
39DAP/reference	0.86185	0.015
41DAP/reference	0.84918	0.028
42DAP/reference	0.80153	0.01
43DAP/reference	0.84266	0.014
47DAP/reference	0.91473	0.293
52DAP/reference	0.78637	0.012
57DAP/reference	0.77943	0.007

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.47097	0.007
17DAP/reference	0.46865	0.004
27DAP/reference	0.89266	0.257
39DAP/reference	0.97425	0.455
41DAP/reference	1.03698	0.846
42DAP/reference	0.98652	0.534
43DAP/reference	0.56653	0.031
47DAP/reference	0.73785	0.012
52DAP/reference	0.86674	0.047
57DAP/reference	0.46139	0.007

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.80903	0.063
17DAP/reference	0.822	0.224
27DAP/reference	0.89022	0.038
39DAP/reference	0.83033	0.013
41DAP/reference	0.87589	0.05
42DAP/reference	1.13108	0.863
43DAP/reference	1.09537	0.768
47DAP/reference	0.92757	0.325
52DAP/reference	0.70508	0.066
57DAP/reference	2.43957	0.017

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.22565	0.817
26DAP/20DAP	0.91691	1
34DAP/26DAP	1.25103	0.819
51DAP/34DAP	0.84082	0.442
52DAP/51DAP	0.74565	1
53DAP/52DAP	0.87633	0.64
55DAP/53DAP	1.07499	0.922
57DAP/55DAP	0.50627	0.127
62DAP/57DAP	1.73643	0.217
68DAP/62DAP	8.13517	0.047
68DAP/14DAP	9.74351	0.018

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.89568	0.322

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	4.71543
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	4.97271
Mature Eggplant/Ripe Tomato	2.24988

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	0.89282	1
12-2/M82	N/A	N/A
12-4/M82	1.10108
1-3/M82	0.71027
2-1-1/M82	N/A	N/A
2-1/M82	N/A	N/A
2-6/M82	1.21694
3-2/M82	N/A	N/A
4-1-1/M82	0.90363
4-1/M82	N/A	N/A
4-3-2/M82	N/A	N/A
4-3/M82	N/A	N/A
5-3/M82	0.91329	0.364
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	1.26938
7-2/M82	N/A	N/A
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.04164	1
IL2-6/WTpooled	1.14136	0.659
IL7-5/WTpooled	0.87315	1
IL7-3/WTpooled	0.9287	0.418
IL12-4/WTpooled	1.14911	0.673
IL1-4/WTpooled	0.93344	0.834
WT/WTpooled	0.99469	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	1.19278	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.90722	0.849
DC3000/delta hrp 6h	N/A	N/A
DC3000/delta hrp 12h	0.52138
DC3000/delta hrp 24h	1.03171	0.71

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.53299	0.032
DC3000 delta B/DC3000 delta AB	0.45089	0.02

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	1.04923	1
Var 0h	1.1171	1
Var 12h I row2-row1	0.73664	0.363
Var 12h NI row2-row1	1.00238	1
Var 36h I row2-row1	0.99203	1
Var 36h NI row2-row1	1.13627	0.482
Var 60h I row2-row1	1.43705	0.543
Var 60h NI row2-row1	1.01086	1
Time course 0hI-0hNI	1.06504	0.799
Time course 12hI-12hNI	1.03305	0.747
Time course 36hI-36hNI	0.87919	0.136
Time course 60hI-60hNI	0.12445	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)	2.44376	0.482
transgenic ySAMdc/azygous control (breaker)	1.37527	0.178
transgenic ySAMdc/azygous control (red)	1.70648	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.97039	0.286

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.48272	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.88297	1
Manapal/WT (break)	1.14752	1
Manapal/WT (red)	1.41529	0.15