Tomato Functional Genomics Database (TFGD)

Expression of 1-1-8.3.11.18

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.07772	0.863
27DAP/17DAP	0.89803	0.796
39DAP/27DAP	1.34929	0.426
41DAP/39DAP	0.82793	0.379
42DAP/41DAP	1.37418	0.696
43DAP/42DAP	1.00054	0.937
47DAP/43DAP	1.15278	0.668
52DAP/47DAP	1.73965	0.601
57DAP/52DAP	1.17732	0.969

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.85769	0.074
17DAP/reference	1.0288	0.528
27DAP/reference	1.01057	0.925
39DAP/reference	0.99305	0.874
41DAP/reference	0.97076	0.667
42DAP/reference	0.8751	0.007
43DAP/reference	1.01412	0.942
47DAP/reference	0.94913	0.083
52DAP/reference	0.8002	0.111
57DAP/reference	0.72052	0.054

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.89635	0.484
27DAP/17DAP	0.93786	0.724
39DAP/27DAP	0.89401	0.4
41DAP/39DAP	0.92614	0.781
42DAP/41DAP	0.99111	0.83
43DAP/42DAP	0.98034	0.854
47DAP/43DAP	1.06015	0.865
52DAP/47DAP	1.235	0.46
57DAP/52DAP	1.16301	0.33
57DAP/7DAP	0.82703	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.38745	0.049
17DAP/reference	1.39538	0.007
27DAP/reference	1.35615	0.107
39DAP/reference	1.25769	0.014
41DAP/reference	1.6105	0.014
42DAP/reference	1.66682	0.007
43DAP/reference	1.57613	0.007
47DAP/reference	0.80582	0.222
52DAP/reference	1.46545	0.01
57DAP/reference	1.24857	0.018

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.16149	0.36
17DAP/reference	1.01016	0.979
27DAP/reference	0.7679	0.1
39DAP/reference	0.91448	0.348
41DAP/reference	0.80404	0.045
42DAP/reference	0.83969	0.073
43DAP/reference	0.98015	0.62
47DAP/reference	0.92426	0.087
52DAP/reference	0.94108	0.22
57DAP/reference	1.11187	0.462

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.16759	0.06
17DAP/reference	1.19237	0.496
27DAP/reference	1.34052	0.156
39DAP/reference	8.42887	0.189
41DAP/reference	1.21219	0.286
42DAP/reference	1.26327	0.07
43DAP/reference	0.84194	0.165
47DAP/reference	0.91588	0.306
52DAP/reference	1.1973	0.42
57DAP/reference	0.54002	0.02

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.99032	1
26DAP/20DAP	0.87372	0.228
34DAP/26DAP	1.05013	1
51DAP/34DAP	1.11519	0.377
52DAP/51DAP	1.37406	0.404
53DAP/52DAP	0.65157	0.063
55DAP/53DAP	1.15114	0.622
57DAP/55DAP	0.6971	0.141
62DAP/57DAP	1.31908	0.303
68DAP/62DAP	1.47947	0.455
68DAP/14DAP	1.18821	0.958

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.47339	0.02

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.71926	0.199
Mature Green Tomato/Ripe Tomato	0.86237	0.446
Immature Eggplant/Mature Eggplant	1.41368	0.053
Ripe Pepper/Ripe Tomato	1.61276	1
Mature Eggplant/Ripe Tomato	1.77678	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.49608	0.536
1-1-2/M82	1.05027	1
12-2/M82	1.15961	1
12-4/M82	0.86342	0.358
1-3/M82	0.96503
2-1-1/M82	1.19929
2-1/M82	N/A	N/A
2-6/M82	1.1572	0.329
3-2/M82	0.9835
4-1-1/M82	1.24971	1
4-1/M82	1.12144
4-3-2/M82	1.08862	1
4-3/M82	1.11489	1
5-3/M82	0.87518	0.642
6-2/M82	1.07351
6-3/M82	0.97762	1
7-1/M82	0.95855	0.803
7-2/M82	1.1544	1
9-3-2/M82	1.7413

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.41522	0.212
IL2-6/WTpooled	1.56003	0.395
IL7-5/WTpooled	1.16008	0.792
IL7-3/WTpooled	1.16641	1
IL12-4/WTpooled	0.6282	1
IL1-4/WTpooled	0.86839	0.699
WT/WTpooled	1.13251	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	1.23546	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.10896	0.921
DC3000/delta hrp 6h	0.89368	0.95
DC3000/delta hrp 12h	0.98212	1
DC3000/delta hrp 24h	0.87819	0.19

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.75046	0.031
DC3000 delta B/DC3000 delta AB	0.79214	0.073

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.93665	0.328
Exp 36h	0.99265	1
Exp 60h	1.20833	1

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

hybridization	ratio	FDR (corrected p value)
self-self	0.99024	1
Var 0h	1.04102	1
Var 12h I row2-row1	0.83171	0.338
Var 12h NI row2-row1	0.98579	0.906
Var 36h I row2-row1	1.07082	0.742
Var 36h NI row2-row1	1.12226	0.482
Var 60h I row2-row1	0.86662	0.439
Var 60h NI row2-row1	1.05186	0.904
Time course 0hI-0hNI	1.10939	0.537
Time course 12hI-12hNI	0.90628	0.247
Time course 36hI-36hNI	0.7531	0.023
Time course 60hI-60hNI	0.3888	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)	1.02568	0.511
transgenic ySAMdc/azygous control (breaker)	0.99863	1
transgenic ySAMdc/azygous control (red)	0.93264	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.04302	0.077

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.56555	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.92112	1
Manapal/WT (break)	0.97945	1
Manapal/WT (red)	0.80192	0.181