Tomato Functional Genomics Database (TFGD)

Expression of 1-1-6.3.9.2

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.42364	0.019
27DAP/17DAP	0.82055	0.532
39DAP/27DAP	1.33728	0.493
41DAP/39DAP	0.71558	0.113
42DAP/41DAP	1.09102	0.937
43DAP/42DAP	1.50335	0.199
47DAP/43DAP	0.47398	0.049
52DAP/47DAP	1.00451	0.963
57DAP/52DAP	0.91615	0.912

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.61477	0.007
17DAP/reference	1.00049	0.819
27DAP/reference	1.1163	0.306
39DAP/reference	1.03014	0.771
41DAP/reference	1.08209	0.667
42DAP/reference	1.23951	0.001
43DAP/reference	0.80434	0.103
47DAP/reference	0.71188	0.001
52DAP/reference	0.82137	0.115
57DAP/reference	0.92291	0.131

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.51717	0.03
27DAP/17DAP	1.17851	0.253
39DAP/27DAP	0.96742	0.759
41DAP/39DAP	0.77533	0.074
42DAP/41DAP	0.98399	0.784
43DAP/42DAP	1.43613	0.013
47DAP/43DAP	0.86439	0.192
52DAP/47DAP	0.89026	0.553
57DAP/52DAP	1.09721	0.543
57DAP/7DAP	0.51339	0.219

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	2.58318	0.024
17DAP/reference	1.63853	0.01
27DAP/reference	0.95278	0.264
39DAP/reference	1.27763	0.033
41DAP/reference	0.8373	0.043
42DAP/reference	1.27158	0.132
43DAP/reference	0.70645	0.02
47DAP/reference	1.13329	0.48
52DAP/reference	0.47455	0.011
57DAP/reference	0.41208	0.006

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.48489	0.077
17DAP/reference	1.86116	0.008
27DAP/reference	1.12772	0.412
39DAP/reference	0.95414	0.281
41DAP/reference	0.95543	0.357
42DAP/reference	1.27974	0.009
43DAP/reference	0.91197	0.37
47DAP/reference	1.1482	0.247
52DAP/reference	0.99757	0.666
57DAP/reference	0.77162	0.063

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.49461	0.016
17DAP/reference	1.65074	0.166
27DAP/reference	1.28018	0.081
39DAP/reference	1.11449	0.203
41DAP/reference	0.94419	0.459
42DAP/reference	1.42824	0.018
43DAP/reference	1.03434	0.894
47DAP/reference	0.46372	0.004
52DAP/reference	0.96349	0.351
57DAP/reference	0.87939	0.217

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.13194	1
26DAP/20DAP	1.18166	0.504
34DAP/26DAP	1.09963	1
51DAP/34DAP	1.5583	0.054
52DAP/51DAP	0.88076	1
53DAP/52DAP	1.10669	0.753
55DAP/53DAP	0.92587	0.5
57DAP/55DAP	1.04121	0.851
62DAP/57DAP	1.04307	0.833
68DAP/62DAP	0.8907	0.505
68DAP/14DAP	1.22394	0.936

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	2.02987	0.018

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.45353
Mature Green Tomato/Ripe Tomato	2.2145	0.058
Immature Eggplant/Mature Eggplant	1.00062	1
Ripe Pepper/Ripe Tomato	0.58567	0.224
Mature Eggplant/Ripe Tomato	2.51435	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	0.91612
12-2/M82	N/A	N/A
12-4/M82	0.55685	0.25
1-3/M82	4.04955
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	1.01204	1
4-3-2/M82	0.8778	1
4-3/M82	1.18826	1
5-3/M82	2.33593	1
6-2/M82	4.25514
6-3/M82	N/A	N/A
7-1/M82	0.83045
7-2/M82	N/A	N/A
9-3-2/M82	0.92587

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.14048	0.277
IL2-6/WTpooled	1.11847	0.427
IL7-5/WTpooled	1.0266	1
IL7-3/WTpooled	0.93199	1
IL12-4/WTpooled	1.13669	0.466
IL1-4/WTpooled	1.01991	1
WT/WTpooled	1.07525	0.686

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	1.16069	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.94684	0.294
DC3000/delta hrp 6h	0.79854	0.942
DC3000/delta hrp 12h	1.21243	1
DC3000/delta hrp 24h	0.54241	0.034

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.49872	0.024
DC3000 delta B/DC3000 delta AB	0.50276	0.02

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.79759	0.328
Exp 36h	0.75561	0.419
Exp 60h	0.65278	0.259

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

hybridization	ratio	FDR (corrected p value)
self-self	1.01226	1
Var 0h	1.08778	0.782
Var 12h I row2-row1	0.86843	0.338
Var 12h NI row2-row1	0.62345	0.349
Var 36h I row2-row1	0.84021	0.805
Var 36h NI row2-row1	1.59514	1
Var 60h I row2-row1	1.01588	1
Var 60h NI row2-row1	1.37372	0.793
Time course 0hI-0hNI	0.69676	0.044
Time course 12hI-12hNI	1.1775	0.155
Time course 36hI-36hNI	1.01701	0.881
Time course 60hI-60hNI	0.3257	0.006

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)	1.17493	0.213
transgenic ySAMdc/azygous control (breaker)	1.17614	0.248
transgenic ySAMdc/azygous control (red)	0.79884	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.03812	0.148

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.34616	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.49369	0.14
Manapal/WT (break)	1.218	1
Manapal/WT (red)	1.19504	1