Tomato Functional Genomics Database (TFGD)

Expression of 1-1-4.4.4.20

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.12696	0.602
27DAP/17DAP	0.91365	0.819
39DAP/27DAP	0.81856	0.425
41DAP/39DAP	1.18543	0.416
42DAP/41DAP	0.94614	1
43DAP/42DAP	0.94381	0.877
47DAP/43DAP	1.16487	0.668
52DAP/47DAP	1.20394	0.654
57DAP/52DAP	1.07801	0.946

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.05677	0.587
17DAP/reference	1.04889	0.127
27DAP/reference	1.05803	0.271
39DAP/reference	0.9385	0.412
41DAP/reference	1.12757	0.026
42DAP/reference	0.98138	0.25
43DAP/reference	0.97746
47DAP/reference	0.98783	0.503
52DAP/reference	0.94453	0.371
57DAP/reference	N/A	N/A

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.04744	1
27DAP/17DAP	0.82529	0.39
39DAP/27DAP	1.07926	0.691
41DAP/39DAP	0.97136	0.968
42DAP/41DAP	0.96108	0.635
43DAP/42DAP	0.98004	0.774
47DAP/43DAP	1.03281	0.951
52DAP/47DAP	0.89519	0.507
57DAP/52DAP	0.9192	0.591
57DAP/7DAP	0.82076	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.9297	0.066
17DAP/reference	0.92745	0.012
27DAP/reference	0.9236	0.012
39DAP/reference	0.95383	0.039
41DAP/reference	0.94045	0.203
42DAP/reference	0.99032	0.554
43DAP/reference	0.98538	0.527
47DAP/reference	0.92606	0.222
52DAP/reference	0.96202	0.304
57DAP/reference	0.97001	0.353

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.16383	0.047
17DAP/reference	1.04035	0.357
27DAP/reference	1.00447	1
39DAP/reference	0.95272	0.243
41DAP/reference	0.94758	0.124
42DAP/reference	0.96274	0.321
43DAP/reference	1.07587	0.407
47DAP/reference	0.92149	0.043
52DAP/reference	0.96864	0.22
57DAP/reference	1.0224	0.755

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.93725	0.268
17DAP/reference	0.98566	0.658
27DAP/reference	0.92613	0.119
39DAP/reference	0.9256	0.025
41DAP/reference	0.9255	0.026
42DAP/reference	0.85843	0.023
43DAP/reference	0.89353	0.106
47DAP/reference	0.94351	0.054
52DAP/reference	0.87068	0.18
57DAP/reference	0.75784	0.024

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.97721	1
26DAP/20DAP	1.00204	1
34DAP/26DAP	0.97409	0.94
51DAP/34DAP	1.08352	0.854
52DAP/51DAP	1.57741	0.522
53DAP/52DAP	1.11715	0.753
55DAP/53DAP	1.07467	0.798
57DAP/55DAP	1.8428	0.461
62DAP/57DAP	1.14707	0.445
68DAP/62DAP	0.8813	0.505
68DAP/14DAP	0.96033	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.80772	0.211

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.72413	0.194
Mature Green Tomato/Ripe Tomato	1.14435	0.478
Immature Eggplant/Mature Eggplant	0.65441	0.062
Ripe Pepper/Ripe Tomato	2.28264	1
Mature Eggplant/Ripe Tomato	2.12191	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.96116	0.944
1-1-2/M82	1.02931	1
12-2/M82	0.98369	0.955
12-4/M82	0.9827
1-3/M82	0.97765	0.378
2-1-1/M82	1.41397	0.764
2-1/M82	N/A	N/A
2-6/M82	1.03542	0.695
3-2/M82	1.0459	1
4-1-1/M82	0.84506	1
4-1/M82	0.99642
4-3-2/M82	0.80394	0.487
4-3/M82	0.87419	1
5-3/M82	1.11422	1
6-2/M82	0.96481
6-3/M82	0.85877
7-1/M82	0.95204	1
7-2/M82	0.98987	1
9-3-2/M82	0.98779

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.19168	1
IL2-6/WTpooled	0.99723	1
IL7-5/WTpooled	0.94992	1
IL7-3/WTpooled	0.85513	1
IL12-4/WTpooled	1.14347	0.503
IL1-4/WTpooled	1.01167	1
WT/WTpooled	1.09104	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	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.0674	0.921
DC3000/delta hrp 6h	1.01469	1
DC3000/delta hrp 12h	1.03781	1
DC3000/delta hrp 24h	0.88359	0.323

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.99613	1
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	0.88965	1
Exp 36h	0.75882	0.539
Exp 60h	0.71734	0.386

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

hybridization	ratio	FDR (corrected p value)
self-self	N/A	N/A
Var 0h	1.061	0.936
Var 12h I row2-row1	N/A	N/A
Var 12h NI row2-row1	N/A	N/A
Var 36h I row2-row1	N/A	N/A
Var 36h NI row2-row1	N/A	N/A
Var 60h I row2-row1	N/A	N/A
Var 60h NI row2-row1	N/A	N/A
Time course 0hI-0hNI	N/A	N/A
Time course 12hI-12hNI	N/A	N/A
Time course 36hI-36hNI	N/A	N/A
Time course 60hI-60hNI	N/A	N/A

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)	0.99243	0.789
transgenic ySAMdc/azygous control (breaker)	1.03785	1
transgenic ySAMdc/azygous control (red)	1.22656	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.0616	0.04

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.91343	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	2.5037	0.086
Manapal/WT (break)	1.89128	0.381
Manapal/WT (red)	1.93239	0.126