Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.1.16.17

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.11736	0.755
27DAP/17DAP	0.92752	0.863
39DAP/27DAP	1.06001	0.922
41DAP/39DAP	0.97549	0.868
42DAP/41DAP	1.21224	0.886
43DAP/42DAP	0.97436	0.895
47DAP/43DAP	1.07014	0.999
52DAP/47DAP	0.91156	0.685
57DAP/52DAP	1.26498	0.941

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.95945	0.442
17DAP/reference	1.04426	0.117
27DAP/reference	1.05024	0.143
39DAP/reference	1.05128	0.318
41DAP/reference	0.9974	1
42DAP/reference	0.93861	0.038
43DAP/reference	0.98174	0.691
47DAP/reference	1.01813	0.685
52DAP/reference	0.98983	0.636
57DAP/reference	0.99558	0.701

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.9648	0.679
27DAP/17DAP	1.06749	0.942
39DAP/27DAP	1.41057	0.057
41DAP/39DAP	1.11918	0.781
42DAP/41DAP	1.2959	0.013
43DAP/42DAP	0.95878	0.684
47DAP/43DAP	1.93466	0.013
52DAP/47DAP	1.10194	0.804
57DAP/52DAP	1.55998	0.05
57DAP/7DAP	1.71779	0.365

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.40254	0.16
17DAP/reference	1.86041	0.006
27DAP/reference	2.0393	0.006
39DAP/reference	2.20279	0.006
41DAP/reference	2.34474	0.019
42DAP/reference	2.40214	0.007
43DAP/reference	2.08187	0.006
47DAP/reference	1.50679	0.345
52DAP/reference	2.01135	0.007
57DAP/reference	2.0776	0.004

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.00052	1
17DAP/reference	0.9587	0.269
27DAP/reference	0.90493	0.134
39DAP/reference	0.93981	0.156
41DAP/reference	0.95564	0.268
42DAP/reference	0.78005	0.035
43DAP/reference	0.88423	0.196
47DAP/reference	0.94498	0.102
52DAP/reference	1.01989	0.194
57DAP/reference	0.98494	0.61

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.54482	0.072
17DAP/reference	1.19082	0.522
27DAP/reference	1.7047	0.028
39DAP/reference	1.44015	0.017
41DAP/reference	1.43886	0.074
42DAP/reference	1.66809	0.08
43DAP/reference	1.65003	0.074
47DAP/reference	0.91988	0.161
52DAP/reference	1.88607	0.106
57DAP/reference	1.23947	0.971

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.01792	0.966
26DAP/20DAP	0.80115	0.512
34DAP/26DAP	1.19101	0.819
51DAP/34DAP	1.48952	0.281
52DAP/51DAP	1.16132	0.467
53DAP/52DAP	1.36579	0.261
55DAP/53DAP	1.26936	0.387
57DAP/55DAP	1.11459	0.927
62DAP/57DAP	0.86039	0.28
68DAP/62DAP	1.07721	0.869
68DAP/14DAP	1.01866	0.958

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.23597	0.077

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.33638	0.081
Mature Green Tomato/Ripe Tomato	0.8856	0.66
Immature Eggplant/Mature Eggplant	1.92411	0.066
Ripe Pepper/Ripe Tomato	0.7084
Mature Eggplant/Ripe Tomato	2.20198	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.95639	0.944
1-1-2/M82	0.95979
12-2/M82	0.93171	0.721
12-4/M82	1.12535	0.476
1-3/M82	0.87636	1
2-1-1/M82	0.98401	1
2-1/M82	N/A	N/A
2-6/M82	1.13627	0.505
3-2/M82	0.98088
4-1-1/M82	0.99578	1
4-1/M82	1.12207
4-3-2/M82	0.81052
4-3/M82	0.89647	1
5-3/M82	0.98053	1
6-2/M82	0.98259
6-3/M82	1.3946
7-1/M82	N/A	N/A
7-2/M82	1.01378	1
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.23288	0.365
IL2-6/WTpooled	0.76548	0.383
IL7-5/WTpooled	1.52577
IL7-3/WTpooled	1.50103	1
IL12-4/WTpooled	1.06099	0.367
IL1-4/WTpooled	0.9786	1
WT/WTpooled	1.05908	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	1.25992	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.95073	1
DC3000/delta hrp 6h	1.18502	1
DC3000/delta hrp 12h	1.0287	1
DC3000/delta hrp 24h	0.91759	0.503

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.86206	0.076
DC3000 delta B/DC3000 delta AB	1.49117	0.141

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.05082	1
Exp 36h	1.24968	0.693
Exp 60h	1.38911	0.399

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

hybridization	ratio	FDR (corrected p value)
self-self	0.99679	1
Var 0h	1.42764	0.936
Var 12h I row2-row1	0.94544	0.565
Var 12h NI row2-row1	1.50783	0.649
Var 36h I row2-row1	0.72636	0.805
Var 36h NI row2-row1	4.96185
Var 60h I row2-row1	N/A	N/A
Var 60h NI row2-row1	1.07396	1
Time course 0hI-0hNI	1.07144	0.852
Time course 12hI-12hNI	1.32025	0.209
Time course 36hI-36hNI	1.69655	0.01
Time course 60hI-60hNI	3.19832	0.008

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)	0.89061	0.286
transgenic ySAMdc/azygous control (breaker)	0.81704	0.142
transgenic ySAMdc/azygous control (red)	1.15404	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.98042	0.172

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.85395	0.268

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.80081	1
Manapal/WT (break)	0.5747	0.297
Manapal/WT (red)	0.95184	0.728