Tomato Functional Genomics Database (TFGD)

Expression of 1-1-4.4.2.12

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.8775	0.427
27DAP/17DAP	0.91967	0.801
39DAP/27DAP	0.77614	0.392
41DAP/39DAP	1.15234	0.535
42DAP/41DAP	1.30349	0.232
43DAP/42DAP	1.06757	1
47DAP/43DAP	1.42277	0.195
52DAP/47DAP	0.91171	0.757
57DAP/52DAP	0.77618	0.473

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.99803	0.727
17DAP/reference	1.06059	0.193
27DAP/reference	1.04291	0.339
39DAP/reference	1.00266	0.857
41DAP/reference	1.04422	0.133
42DAP/reference	0.99734	0.587
43DAP/reference	1.01267	0.812
47DAP/reference	0.94165	0.071
52DAP/reference	1.09348	0.076
57DAP/reference	0.9698	0.294

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.14841	0.699
27DAP/17DAP	1.15322	0.518
39DAP/27DAP	0.97416	0.859
41DAP/39DAP	0.95665	0.934
42DAP/41DAP	1.02996	1
43DAP/42DAP	0.87904	0.216
47DAP/43DAP	1.10583	0.822
52DAP/47DAP	1.02861	0.907
57DAP/52DAP	0.70613	0.119
57DAP/7DAP	1.02558	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.0531	0.491
17DAP/reference	1.17109	0.134
27DAP/reference	1.18865	0.06
39DAP/reference	1.31408	0.252
41DAP/reference	1.30279	0.023
42DAP/reference	1.29939	0.03
43DAP/reference	1.36509	0.056
47DAP/reference	0.98831	0.671
52DAP/reference	1.1497	0.055
57DAP/reference	1.37124	0.006

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.12776	0.325
17DAP/reference	1.13509	0.079
27DAP/reference	1.12353	0.303
39DAP/reference	1.0174	0.978
41DAP/reference	1.0452	1
42DAP/reference	0.90203	0.03
43DAP/reference	1.14892	0.176
47DAP/reference	0.96842	0.338
52DAP/reference	1.07647	0.046
57DAP/reference	1.06264	0.462

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.94683	0.29
17DAP/reference	1.15399	0.503
27DAP/reference	1.24504	0.075
39DAP/reference	1.28228	0.021
41DAP/reference	1.18831	0.168
42DAP/reference	1.09388	0.333
43DAP/reference	0.99241	0.66
47DAP/reference	0.94621	0.168
52DAP/reference	0.95602	0.582
57DAP/reference	1.10093	0.625

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.88041	1
26DAP/20DAP	0.68514	0.512
34DAP/26DAP	1.256	0.819
51DAP/34DAP	1.11898	0.241
52DAP/51DAP	0.75879	0.151
53DAP/52DAP	0.92662	0.732
55DAP/53DAP	1.19569	0.341
57DAP/55DAP	1.0015	0.961
62DAP/57DAP	0.89533	0.466
68DAP/62DAP	1.03681	1
68DAP/14DAP	0.82341	0.08

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.63619	0.043

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.22122	0.089
Mature Green Tomato/Ripe Tomato	0.91557	0.411
Immature Eggplant/Mature Eggplant	1.17836	0.334
Ripe Pepper/Ripe Tomato	1.23638	1
Mature Eggplant/Ripe Tomato	1.76448	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.09947	0.877
1-1-2/M82	0.96634	1
12-2/M82	0.95277	0.955
12-4/M82	0.97592
1-3/M82	0.92478	0.378
2-1-1/M82	0.80591	0.465
2-1/M82	0.86345
2-6/M82	0.8413	1
3-2/M82	0.88394	0.752
4-1-1/M82	0.81	1
4-1/M82	N/A	N/A
4-3-2/M82	0.89946	0.698
4-3/M82	0.86621	0.475
5-3/M82	1.09909	1
6-2/M82	0.62238
6-3/M82	1.23952	1
7-1/M82	0.85279
7-2/M82	0.80827
9-3-2/M82	0.76784

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	0.80411	0.473
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.02065	1
IL12-4/WTpooled	1.01404	1
IL1-4/WTpooled	0.96055
WT/WTpooled	1.04353	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	0.88064	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.01907	1
DC3000/delta hrp 6h	0.99598	0.95
DC3000/delta hrp 12h	0.95655	1
DC3000/delta hrp 24h	0.53754	0.034

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.67776
DC3000 delta B/DC3000 delta AB	0.70893	0.043

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.04743	1
Exp 36h	0.7628	0.504
Exp 60h	0.7252	0.29

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

hybridization	ratio	FDR (corrected p value)
self-self	0.9673	1
Var 0h	1.09891	0.98
Var 12h I row2-row1	0.87196	0.565
Var 12h NI row2-row1	0.86243	0.713
Var 36h I row2-row1	0.94189	0.805
Var 36h NI row2-row1	1.35636	1
Var 60h I row2-row1	1.4542	1
Var 60h NI row2-row1	1.0659	0.904
Time course 0hI-0hNI	0.98164	0.945
Time course 12hI-12hNI	0.90958	0.275
Time course 36hI-36hNI	0.75902	0.023
Time course 60hI-60hNI	0.34178	0.005

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)	0.92233	0.314
transgenic ySAMdc/azygous control (breaker)	1.22045	0.248
transgenic ySAMdc/azygous control (red)	0.95562	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.97698	0.313

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	2.25853	0.222

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.47997	0.105
Manapal/WT (break)	1.28015	0.381
Manapal/WT (red)	0.83566	0.242