Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.2.2.16

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.00973	0.938
27DAP/17DAP	1.11485	0.86
39DAP/27DAP	1.15771	0.56
41DAP/39DAP	0.85941	0.478
42DAP/41DAP	1.17731	0.825
43DAP/42DAP	1.0068	0.937
47DAP/43DAP	1.29674	0.4
52DAP/47DAP	0.85577	0.612
57DAP/52DAP	0.95006	0.919

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.98469	0.601
17DAP/reference	0.83829	0.024
27DAP/reference	1.05113	0.88
39DAP/reference	0.93633	0.333
41DAP/reference	0.80272	0.039
42DAP/reference	0.96657	0.278
43DAP/reference	0.98877	0.82
47DAP/reference	1.18458	0.035
52DAP/reference	1.1738	0.056
57DAP/reference	1.30247	0.05

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.02883	0.899
27DAP/17DAP	1.02432	1
39DAP/27DAP	0.98569	0.908
41DAP/39DAP	1.05238	0.914
42DAP/41DAP	1.06752	0.852
43DAP/42DAP	0.88987	0.132
47DAP/43DAP	1.07351	0.713
52DAP/47DAP	0.99455	0.962
57DAP/52DAP	1.00789	1
57DAP/7DAP	1.37276	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.31086	0.079
17DAP/reference	1.36164	0.007
27DAP/reference	1.13943	0.551
39DAP/reference	1.4748	0.018
41DAP/reference	1.38521	0.028
42DAP/reference	1.33425	0.013
43DAP/reference	1.41829	0.024
47DAP/reference	1.21282	0.142
52DAP/reference	1.30651	0.021
57DAP/reference	1.14924	0.049

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.95119	0.592
17DAP/reference	0.89726	0.062
27DAP/reference	1.09201	0.338
39DAP/reference	0.98394	0.539
41DAP/reference	0.94507	0.34
42DAP/reference	0.9936	0.655
43DAP/reference	0.79017	0.019
47DAP/reference	0.92477	0.232
52DAP/reference	0.77831	0.018
57DAP/reference	0.8374	0.058

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.30118	0.033
17DAP/reference	1.12988	0.641
27DAP/reference	1.3324	0.034
39DAP/reference	1.22497	0.182
41DAP/reference	1.21265	0.083
42DAP/reference	1.18451	0.3
43DAP/reference	1.03659	0.828
47DAP/reference	1.01872	1
52DAP/reference	1.26582	0.198
57DAP/reference	1.4864	0.078

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.98951	1
26DAP/20DAP	1.3158	0.193
34DAP/26DAP	0.92825	0.712
51DAP/34DAP	1.34694	0.07
52DAP/51DAP	1.04126	0.77
53DAP/52DAP	1.20615	0.858
55DAP/53DAP	0.81517	0.293
57DAP/55DAP	1.42285	0.694
62DAP/57DAP	1.14194	1
68DAP/62DAP	1.03361	1
68DAP/14DAP	1.49012	0.087

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.87547	0.378

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.88368	0.426
Mature Green Tomato/Ripe Tomato	0.76867	0.027
Immature Eggplant/Mature Eggplant	1.29021	0.105
Ripe Pepper/Ripe Tomato	1.35117	1
Mature Eggplant/Ripe Tomato	0.88525	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.30597	0.877
1-1-2/M82	1.16106	1
12-2/M82	0.98067	0.955
12-4/M82	0.7633	0.257
1-3/M82	1.56954
2-1-1/M82	0.88061	0.683
2-1/M82	0.93903
2-6/M82	0.85961	1
3-2/M82	1.10818
4-1-1/M82	0.85304	1
4-1/M82	0.89562
4-3-2/M82	0.9811	0.487
4-3/M82	0.91027	1
5-3/M82	1.28075	0.496
6-2/M82	0.85448
6-3/M82	1.07858	1
7-1/M82	0.87267
7-2/M82	1.17359	1
9-3-2/M82	1.27161

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	0.85195	0.473
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.04218	1
IL12-4/WTpooled	0.81269	0.543
IL1-4/WTpooled	0.8884
WT/WTpooled	0.88199	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	0.92969	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.08711	0.921
DC3000/delta hrp 6h	1.00242	0.95
DC3000/delta hrp 12h	0.9435	1
DC3000/delta hrp 24h	0.87288	0.194

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.01403
DC3000 delta B/DC3000 delta AB	0.92123	0.418

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.98705	1
Exp 36h	1.09557	1
Exp 60h	0.94278	0.855

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

hybridization	ratio	FDR (corrected p value)
self-self	1.00989	1
Var 0h	0.69211	0.933
Var 12h I row2-row1	0.96698	0.948
Var 12h NI row2-row1	1.16201	0.34
Var 36h I row2-row1	1.19877	0.298
Var 36h NI row2-row1	0.98169	0.852
Var 60h I row2-row1	0.82566	0.285
Var 60h NI row2-row1	1.05383	0.904
Time course 0hI-0hNI	0.94371	0.612
Time course 12hI-12hNI	0.95736	0.592
Time course 36hI-36hNI	1.23761	0.011
Time course 60hI-60hNI	1.63959	0.012

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)	0.98397	0.789
transgenic ySAMdc/azygous control (breaker)	1.25477	1
transgenic ySAMdc/azygous control (red)	1.09339	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.9357	0.286

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.90941	0.308

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.98157	1
Manapal/WT (break)	0.97776	1
Manapal/WT (red)	0.92349	0.503