Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.3.7.17

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.99929	0.867
27DAP/17DAP	0.92361	0.787
39DAP/27DAP	1.23187	0.466
41DAP/39DAP	0.92306	0.711
42DAP/41DAP	1.27474	0.719
43DAP/42DAP	1.10935	0.982
47DAP/43DAP	1.05849	0.926
52DAP/47DAP	0.88629	0.651
57DAP/52DAP	1.14712	0.912

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.94162	0.159
17DAP/reference	1.01031	0.74
27DAP/reference	1.00577	0.996
39DAP/reference	0.97672	0.68
41DAP/reference	0.92868	0.434
42DAP/reference	0.90322	0.004
43DAP/reference	0.97426	0.631
47DAP/reference	0.93757	0.055
52DAP/reference	0.85771	0.111
57DAP/reference	0.75356	0.02

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.94689	0.089
27DAP/17DAP	1.24382	0.077
39DAP/27DAP	0.70844	0.048
41DAP/39DAP	0.86401	0.547
42DAP/41DAP	0.88509	0.173
43DAP/42DAP	0.67321	0.043
47DAP/43DAP	1.04039	0.973
52DAP/47DAP	1.15706	0.478
57DAP/52DAP	1.00854	0.892
57DAP/7DAP	1.17952	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.19121	0.399
17DAP/reference	4.93121	0.042
27DAP/reference	3.31065	0.006
39DAP/reference	3.6316	0.01
41DAP/reference	1.97202	0.054
42DAP/reference	1.29797	0.889
43DAP/reference	0.54908	0.016
47DAP/reference	0.99514	1
52DAP/reference	0.50321	0.019
57DAP/reference	0.63936	0.018

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.85559	0.362
17DAP/reference	0.94707	0.139
27DAP/reference	0.86959	0.115
39DAP/reference	0.93489	0.281
41DAP/reference	0.86011	0.078
42DAP/reference	0.82646	0.023
43DAP/reference	1.23379	0.259
47DAP/reference	0.86723	0.021
52DAP/reference	0.99432	0.666
57DAP/reference	1.11398	0.26

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.31355	0.04
17DAP/reference	1.06357	0.988
27DAP/reference	3.21029	0.056
39DAP/reference	1.98191	0.046
41DAP/reference	1.23959	0.162
42DAP/reference	0.71068	0.041
43DAP/reference	0.59941	0.024
47DAP/reference	1.01387	1
52DAP/reference	0.63957	0.098
57DAP/reference	0.66337	0.049

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.99256	1
26DAP/20DAP	1.1181	0.744
34DAP/26DAP	0.73929	0.164
51DAP/34DAP	0.85698	0.292
52DAP/51DAP	0.89044	1
53DAP/52DAP	1.02908	1
55DAP/53DAP	1.1552	0.452
57DAP/55DAP	1.03618	0.87
62DAP/57DAP	1.08925	0.767
68DAP/62DAP	1.16702	0.507
68DAP/14DAP	1.118	0.889

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.85675	0.269

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.77128
Mature Green Tomato/Ripe Tomato	1.15203	0.948
Immature Eggplant/Mature Eggplant	1.29891	0.101
Ripe Pepper/Ripe Tomato	1.37258	1
Mature Eggplant/Ripe Tomato	1.27551	0.373

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	N/A	N/A
12-2/M82	N/A	N/A
12-4/M82	0.89472	1
1-3/M82	N/A	N/A
2-1-1/M82	N/A	N/A
2-1/M82	N/A	N/A
2-6/M82	N/A	N/A
3-2/M82	N/A	N/A
4-1-1/M82	N/A	N/A
4-1/M82	N/A	N/A
4-3-2/M82	1.02849
4-3/M82	N/A	N/A
5-3/M82	0.94539	1
6-2/M82	1.20555
6-3/M82	N/A	N/A
7-1/M82	1.06873	0.598
7-2/M82	1.21399	0.385
9-3-2/M82	1.04834

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	0.94418
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.42902	1
IL12-4/WTpooled	0.86489	0.71
IL1-4/WTpooled	1.11246
WT/WTpooled	1.0758	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	0.9889	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.97502	1
DC3000/delta hrp 6h	1.73062	1
DC3000/delta hrp 12h	1.13872	1
DC3000/delta hrp 24h	0.84628	0.057

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.69135	0.023
DC3000 delta B/DC3000 delta AB	1.6572	0.084

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.9829	1
Exp 36h	1.18127	0.489
Exp 60h	1.16165	0.22

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

hybridization	ratio	FDR (corrected p value)
self-self	1.05328	1
Var 0h	1.022	1
Var 12h I row2-row1	1.22278	0.379
Var 12h NI row2-row1	0.85185	0.713
Var 36h I row2-row1	0.83877	1
Var 36h NI row2-row1	1.53202	0.482
Var 60h I row2-row1	0.79138	0.285
Var 60h NI row2-row1	1.13631	0.904
Time course 0hI-0hNI	1.17258	0.63
Time course 12hI-12hNI	0.90696	0.212
Time course 36hI-36hNI	0.74736	0.033
Time course 60hI-60hNI	0.95672	0.646

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)	0.88448	0.299
transgenic ySAMdc/azygous control (breaker)	0.94869	1
transgenic ySAMdc/azygous control (red)	1.10452	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.98665	0.208

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.90099	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.99252	1
Manapal/WT (break)	1.49206	0.183
Manapal/WT (red)	1.06547	1