Tomato Functional Genomics Database (TFGD)

Expression of 1-1-4.4.9.17

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.11125	0.697
27DAP/17DAP	0.97351	0.918
39DAP/27DAP	0.77803	0.304
41DAP/39DAP	0.79413	0.478
42DAP/41DAP	1.11442	0.978
43DAP/42DAP	1.12364	1
47DAP/43DAP	1.1252	0.563
52DAP/47DAP	1.33026	0.965
57DAP/52DAP	1.29977	0.894

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.11551	0.587
17DAP/reference	1.18671	0.014
27DAP/reference	0.98429	0.711
39DAP/reference	1.07542	0.132
41DAP/reference	1.09679	0.133
42DAP/reference	0.81347	0.002
43DAP/reference	1.11778	0.34
47DAP/reference	0.8938	0.03
52DAP/reference	0.7768	0.073
57DAP/reference	0.78914	0.038

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.20521	0.284
27DAP/17DAP	1.03839	0.957
39DAP/27DAP	1.03734	0.654
41DAP/39DAP	0.96846	0.959
42DAP/41DAP	0.89562	0.524
43DAP/42DAP	0.93867	0.447
47DAP/43DAP	1.10199	0.744
52DAP/47DAP	1.12696	0.603
57DAP/52DAP	1.00951	0.921
57DAP/7DAP	1.03322	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.10252	0.377
17DAP/reference	1.20347	0.032
27DAP/reference	1.08247	0.551
39DAP/reference	0.94979	0.354
41DAP/reference	0.91539	0.259
42DAP/reference	0.74225	0.023
43DAP/reference	1.08326	0.307
47DAP/reference	1.00327	1
52DAP/reference	0.86136	0.083
57DAP/reference	1.00094	0.629

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.28256	0.052
17DAP/reference	1.2023	0.092
27DAP/reference	1.00958	0.765
39DAP/reference	0.8923	0.105
41DAP/reference	0.78308	0.017
42DAP/reference	0.728	0.039
43DAP/reference	1.1733	0.633
47DAP/reference	0.82967	0.021
52DAP/reference	1.06053	0.789
57DAP/reference	1.30514	0.123

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.21632	0.119
17DAP/reference	1.08408	0.538
27DAP/reference	1.1786	0.237
39DAP/reference	1.08546	0.365
41DAP/reference	0.98397	0.618
42DAP/reference	0.99153	0.816
43DAP/reference	0.92112	0.348
47DAP/reference	1.00158	0.708
52DAP/reference	2.04514	0.136
57DAP/reference	0.7364	0.048

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.09919	0.786
26DAP/20DAP	1.39709	0.197
34DAP/26DAP	1.01217	0.961
51DAP/34DAP	1.25924	0.565
52DAP/51DAP	0.97698	1
53DAP/52DAP	1.13255	0.594
55DAP/53DAP	1.05009	1
57DAP/55DAP	1.2075	0.51
62DAP/57DAP	1.41277	0.257
68DAP/62DAP	0.67861	0.037
68DAP/14DAP	0.42852	0.086

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.25525	0.162

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	1.29814	0.835
Immature Eggplant/Mature Eggplant	2.56264	0.222
Ripe Pepper/Ripe Tomato	0.63112	0.224
Mature Eggplant/Ripe Tomato	0.83902	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.93611	0.944
1-1-2/M82	0.95587	1
12-2/M82	1.03264	1
12-4/M82	1.09503
1-3/M82	0.83599	0.501
2-1-1/M82	1.18679	0.764
2-1/M82	N/A	N/A
2-6/M82	1.1542	0.695
3-2/M82	1.15085	0.967
4-1-1/M82	1.2124	0.968
4-1/M82	N/A	N/A
4-3-2/M82	0.99151
4-3/M82	1.00026	1
5-3/M82	1.03606	1
6-2/M82	1.04447
6-3/M82	0.85079	0.982
7-1/M82	1.08302
7-2/M82	1.15785	1
9-3-2/M82	1.13897

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.04115	1
IL2-6/WTpooled	0.86765	0.473
IL7-5/WTpooled	1.07938
IL7-3/WTpooled	1.00053	1
IL12-4/WTpooled	1.25034	0.525
IL1-4/WTpooled	0.80956
WT/WTpooled	0.9751	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	0.6155	0.256

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.01258	1
DC3000/delta hrp 6h	0.69509	0.81
DC3000/delta hrp 12h	1.02645	1
DC3000/delta hrp 24h	1.01631	0.76

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.31802	0.042
DC3000 delta B/DC3000 delta AB	1.16127	0.544

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.92973	0.265
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	1.02766	1
Var 0h	0.99253	1
Var 12h I row2-row1	1.04273	0.736
Var 12h NI row2-row1	0.99727	1
Var 36h I row2-row1	1.0433	1
Var 36h NI row2-row1	0.77119	0.584
Var 60h I row2-row1	1.02156	1
Var 60h NI row2-row1	1.02908	0.904
Time course 0hI-0hNI	0.99316	1
Time course 12hI-12hNI	1.00752	0.868
Time course 36hI-36hNI	1.07968	0.19
Time course 60hI-60hNI	1.37942	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)	1.17696	0.212
transgenic ySAMdc/azygous control (breaker)	0.98587	1
transgenic ySAMdc/azygous control (red)	1.13579	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.0413	0.1

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.9446	0.431

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.06577	1
Manapal/WT (break)	1.02799	1
Manapal/WT (red)	1.1003	1