Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.1.15.6

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.98297	0.823
27DAP/17DAP	1.1606	0.845
39DAP/27DAP	0.98718	0.782
41DAP/39DAP	1.26473	0.225
42DAP/41DAP	1.1669	0.691
43DAP/42DAP	1.06751	0.948
47DAP/43DAP	1.1858	0.668
52DAP/47DAP	0.98336	0.821
57DAP/52DAP	1.23192	0.907

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.96306	0.562
17DAP/reference	1.06951	0.282
27DAP/reference	1.00295	1
39DAP/reference	1.00535	0.903
41DAP/reference	1.05268	0.171
42DAP/reference	0.96963	0.151
43DAP/reference	0.99254	0.82
47DAP/reference	0.9163	0.083
52DAP/reference	0.8202	0.121
57DAP/reference	0.80028	0.068

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.96593	0.56
27DAP/17DAP	0.9731	0.748
39DAP/27DAP	1.02574	0.685
41DAP/39DAP	1.13032	0.781
42DAP/41DAP	0.9771	0.762
43DAP/42DAP	0.9718	0.522
47DAP/43DAP	1.01388	0.926
52DAP/47DAP	0.99815	0.979
57DAP/52DAP	0.99814	0.905
57DAP/7DAP	1.11283	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.89719	0.183
17DAP/reference	0.88968	0.011
27DAP/reference	0.83135	0.01
39DAP/reference	0.95022	0.023
41DAP/reference	0.93635	0.082
42DAP/reference	0.92686	0.05
43DAP/reference	0.85082	0.016
47DAP/reference	0.86571	0.057
52DAP/reference	0.84805	0.013
57DAP/reference	0.88778	0.017

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.07335	0.39
17DAP/reference	1.02247	0.789
27DAP/reference	0.87739	0.119
39DAP/reference	0.90903	0.214
41DAP/reference	0.82267	0.068
42DAP/reference	0.85644	0.15
43DAP/reference	1.09093	0.396
47DAP/reference	0.97813	0.434
52DAP/reference	0.93025	0.187
57DAP/reference	1.11374	0.188

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.93023	0.23
17DAP/reference	0.99797	0.81
27DAP/reference	0.84964	0.031
39DAP/reference	0.84263	0.018
41DAP/reference	0.87302	0.046
42DAP/reference	0.73795	0.036
43DAP/reference	0.86226	0.098
47DAP/reference	0.9162	0.269
52DAP/reference	0.83521	0.15
57DAP/reference	0.55632	0.017

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.94944	0.997
26DAP/20DAP	0.92398	0.512
34DAP/26DAP	0.96387	0.816
51DAP/34DAP	0.9177	0.268
52DAP/51DAP	0.96271	1
53DAP/52DAP	1.0016	0.983
55DAP/53DAP	0.94149	0.632
57DAP/55DAP	0.95051	0.789
62DAP/57DAP	1.05039	0.678
68DAP/62DAP	0.89135	0.7
68DAP/14DAP	0.86451	0.121

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.01614	0.954

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.71222	0.148
Immature Eggplant/Mature Eggplant	1.12665	0.288
Ripe Pepper/Ripe Tomato	0.25995	0.224
Mature Eggplant/Ripe Tomato	0.96153	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.96049	0.944
1-1-2/M82	0.99317	1
12-2/M82	1.08622	1
12-4/M82	1.02802	0.611
1-3/M82	0.73026	0.378
2-1-1/M82	1.01
2-1/M82	1.05618
2-6/M82	1.16813	0.594
3-2/M82	0.8279
4-1-1/M82	0.94683	1
4-1/M82	1.04397
4-3-2/M82	0.93659
4-3/M82	0.94999	1
5-3/M82	0.98025	1
6-2/M82	0.92512
6-3/M82	1.18759	1
7-1/M82	0.73349	0.408
7-2/M82	0.88004	0.881
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.90338	0.243
IL2-6/WTpooled	1.04336	0.659
IL7-5/WTpooled	1.11414	1
IL7-3/WTpooled	0.82508	0.418
IL12-4/WTpooled	0.90532	0.543
IL1-4/WTpooled	0.93866	0.476
WT/WTpooled	1.00165	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	0.86335	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.02068	0.921
DC3000/delta hrp 6h	1.17261	1
DC3000/delta hrp 12h	1.05207	1
DC3000/delta hrp 24h	1.06233	0.516

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.91825	0.151
DC3000 delta B/DC3000 delta AB	0.97001	0.805

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.91989	1
Exp 36h	1.48873	0.693
Exp 60h	1.10598	0.563

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

hybridization	ratio	FDR (corrected p value)
self-self	0.99707	1
Var 0h	1.16865	0.98
Var 12h I row2-row1	1.03117	0.654
Var 12h NI row2-row1	0.99731	1
Var 36h I row2-row1	1.00533	1
Var 36h NI row2-row1	0.92783	0.706
Var 60h I row2-row1	1.24849	0.562
Var 60h NI row2-row1	1.169	0.904
Time course 0hI-0hNI	1.03376	1
Time course 12hI-12hNI	1.06185	0.633
Time course 36hI-36hNI	0.94425	0.156
Time course 60hI-60hNI	1.00506	1

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)	1.00694	1
transgenic ySAMdc/azygous control (breaker)	0.36093	0.131
transgenic ySAMdc/azygous control (red)	1.13266	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.01655	0.525

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.16739	0.237

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.71526	0.172
Manapal/WT (break)	0.53966	0.333
Manapal/WT (red)	0.65904	0.229