Tomato Functional Genomics Database (TFGD)

Expression of 1-1-5.3.11.19

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.07362	0.839
27DAP/17DAP	1.34476	0.769
39DAP/27DAP	1.05085	1
41DAP/39DAP	1.33264	0.722
42DAP/41DAP	1.00448	1
43DAP/42DAP	1.03219	0.937
47DAP/43DAP	1.21377	0.659
52DAP/47DAP	1.13017	0.93
57DAP/52DAP	1.01332	0.971

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.00718	0.727
17DAP/reference	1.14041	0.018
27DAP/reference	0.98601	0.725
39DAP/reference	1.08963	0.132
41DAP/reference	1.07692	0.365
42DAP/reference	0.92267	0.091
43DAP/reference	1.07587	0.569
47DAP/reference	0.83504	0.006
52DAP/reference	0.70752	0.05
57DAP/reference	0.73331	0.015

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.93915	0.697
27DAP/17DAP	0.93974	0.854
39DAP/27DAP	1.13718	0.57
41DAP/39DAP	0.80494	0.347
42DAP/41DAP	1.40819	0.01
43DAP/42DAP	1.55701	0.034
47DAP/43DAP	0.99012	0.985
52DAP/47DAP	0.71597	0.171
57DAP/52DAP	1.1761	0.357
57DAP/7DAP	1.26851	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.98633	0.613
17DAP/reference	0.89023	0.144
27DAP/reference	1.14424	0.107
39DAP/reference	0.72429	0.02
41DAP/reference	0.86692	0.166
42DAP/reference	0.81244	0.034
43DAP/reference	1.13521	0.386
47DAP/reference	0.99147	0.671
52DAP/reference	1.17169	0.212
57DAP/reference	0.97433	0.494

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.10722	0.491
17DAP/reference	1.0207	0.979
27DAP/reference	0.85955	0.195
39DAP/reference	0.83372	0.178
41DAP/reference	0.83685	0.1
42DAP/reference	0.74664	0.055
43DAP/reference	1.27499	0.466
47DAP/reference	0.88112	0.051
52DAP/reference	0.89404	0.101
57DAP/reference	1.13911	0.374

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.8719	0.104
17DAP/reference	0.93799	0.477
27DAP/reference	0.8448	0.102
39DAP/reference	0.8048	0.022
41DAP/reference	0.90747	0.264
42DAP/reference	0.85085	0.172
43DAP/reference	0.67643	0.049
47DAP/reference	0.95199	0.409
52DAP/reference	1.2497	0.609
57DAP/reference	0.57938	0.03

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.16132	0.966
26DAP/20DAP	0.72918
34DAP/26DAP	1.20641	0.819
51DAP/34DAP	1.27186	0.377
52DAP/51DAP	1.54928
53DAP/52DAP	1.00159	0.998
55DAP/53DAP	1.28995	0.671
57DAP/55DAP	1.07599	0.764
62DAP/57DAP	1.1181	0.833
68DAP/62DAP	0.6624	0.211
68DAP/14DAP	0.62865	0.121

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.13335	0.7

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	N/A	N/A
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	2.7563
Mature Eggplant/Ripe Tomato	0.97656

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	1.55184
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	0.6249
4-1/M82	N/A	N/A
4-3-2/M82	N/A	N/A
4-3/M82	N/A	N/A
5-3/M82	N/A	N/A
6-2/M82	N/A	N/A
6-3/M82	0.92875
7-1/M82	N/A	N/A
7-2/M82	N/A	N/A
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	1.42862	0.584
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.95985	1
IL12-4/WTpooled	0.72726	0.71
IL1-4/WTpooled	1.28967
WT/WTpooled	1.06844	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	2.11383	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.06276
DC3000/delta hrp 6h	N/A	N/A
DC3000/delta hrp 12h	1.0783	1
DC3000/delta hrp 24h	0.9807	0.782

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	N/A	N/A
DC3000 delta B/DC3000 delta AB	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.97921	1
Exp 36h	0.8756	0.82
Exp 60h	1.21201	0.399

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

hybridization	ratio	FDR (corrected p value)
self-self	1.03527	1
Var 0h	0.99656	1
Var 12h I row2-row1	1.15622	0.443
Var 12h NI row2-row1	1.10478	1
Var 36h I row2-row1	0.90883	1
Var 36h NI row2-row1	0.84694	0.61
Var 60h I row2-row1	0.88328	0.285
Var 60h NI row2-row1	0.84321	0.977
Time course 0hI-0hNI	0.94906	0.867
Time course 12hI-12hNI	0.98632	0.953
Time course 36hI-36hNI	1.53991	0.023
Time course 60hI-60hNI	1.94532	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)	1.17271	0.339
transgenic ySAMdc/azygous control (breaker)	0.8641	0.49
transgenic ySAMdc/azygous control (red)	0.96646	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.03689	0.045

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.0269	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.83126	1
Manapal/WT (break)	1.19536	0.381
Manapal/WT (red)	0.92891	0.424