Tomato Functional Genomics Database (TFGD)

Expression of 1-1-8.2.4.20

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.1217	0.863
27DAP/17DAP	1.0982	0.902
39DAP/27DAP	1.05879	0.965
41DAP/39DAP	0.91347	0.701
42DAP/41DAP	0.91408	1
43DAP/42DAP	0.96636	0.914
47DAP/43DAP	1.13991	0.584
52DAP/47DAP	1.38761	0.691
57DAP/52DAP	0.72813	0.513

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.88992	0.293
17DAP/reference	0.88326	0.419
27DAP/reference	0.99893	0.923
39DAP/reference	1.07905	0.664
41DAP/reference	1.00735	1
42DAP/reference	0.78411	0.056
43DAP/reference	0.87113	0.054
47DAP/reference	0.94193	0.224
52DAP/reference	0.98522	0.636
57DAP/reference	1.30121

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.13754	0.749
27DAP/17DAP	0.99043	0.919
39DAP/27DAP	0.94	0.668
41DAP/39DAP	1.23939	0.849
42DAP/41DAP	0.67615	0.063
43DAP/42DAP	1.11207	0.585
47DAP/43DAP	0.7026	0.382
52DAP/47DAP	1.30561	0.412
57DAP/52DAP	0.94546	0.732
57DAP/7DAP	1.74172

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.91365	0.157
17DAP/reference	1.06314	0.822
27DAP/reference	1.36909	0.012
39DAP/reference	3.73195	0.007
41DAP/reference	3.49331	0.01
42DAP/reference	4.49699	0.009
43DAP/reference	4.08353	0.035
47DAP/reference	2.18143	0.353
52DAP/reference	3.03649	0.229
57DAP/reference	1.7509	0.268

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.98677	0.869
17DAP/reference	0.7396	0.043
27DAP/reference	0.88122	0.173
39DAP/reference	1.02651	1
41DAP/reference	0.9555	0.403
42DAP/reference	1.06348	0.744
43DAP/reference	1.29807	0.04
47DAP/reference	1.08054	0.441
52DAP/reference	1.0488	0.713
57DAP/reference	0.99813	0.649

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.43753	0.296
17DAP/reference	1.83386	0.212
27DAP/reference	3.93108	0.014
39DAP/reference	2.65528	0.052
41DAP/reference	2.02124	0.06
42DAP/reference	1.3855	0.233
43DAP/reference	1.44594	0.285
47DAP/reference	0.90877	0.278
52DAP/reference	1.51041	0.592
57DAP/reference	1.18735	0.501

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.04109	0.966
26DAP/20DAP	N/A	N/A
34DAP/26DAP	1.10899	1
51DAP/34DAP	1.03152	0.747
52DAP/51DAP	1.01577	1
53DAP/52DAP	1.09713	0.882
55DAP/53DAP	1.87602	0.634
57DAP/55DAP	0.93674	0.817
62DAP/57DAP	1.63511
68DAP/62DAP	1.24513	0.878
68DAP/14DAP	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.96765	0.665

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	5.02908	0.058
Mature Green Tomato/Ripe Tomato	N/A	N/A
Immature Eggplant/Mature Eggplant	0.35973
Ripe Pepper/Ripe Tomato	N/A	N/A
Mature Eggplant/Ripe Tomato	N/A	N/A

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.61469
1-1-2/M82	N/A	N/A
12-2/M82	N/A	N/A
12-4/M82	1.49679	0.563
1-3/M82	0.6184
2-1-1/M82	0.84589
2-1/M82	N/A	N/A
2-6/M82	1.01126
3-2/M82	N/A	N/A
4-1-1/M82	N/A	N/A
4-1/M82	17.6497	0.401
4-3-2/M82	N/A	N/A
4-3/M82	N/A	N/A
5-3/M82	0.91741	1
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
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	1.87314
IL2-6/WTpooled	1.03641
IL7-5/WTpooled	1.31791
IL7-3/WTpooled	2.09916	1
IL12-4/WTpooled	0.90826	0.71
IL1-4/WTpooled	0.68524	0.562
WT/WTpooled	1.21296	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	0.77226	0.216

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.03149	0.921
DC3000/delta hrp 6h	0.94977	0.95
DC3000/delta hrp 12h	0.86702	1
DC3000/delta hrp 24h	1.74892	0.042

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.91415	0.513
DC3000 delta B/DC3000 delta AB	0.7646	0.024

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.36879	1
Exp 36h	1.08307	1
Exp 60h	0.70582	0.386

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

hybridization	ratio	FDR (corrected p value)
self-self	0.94918	1
Var 0h	1.01624	1
Var 12h I row2-row1	0.92391	0.627
Var 12h NI row2-row1	1.07074	1
Var 36h I row2-row1	1.13811	0.601
Var 36h NI row2-row1	1.18903	0.276
Var 60h I row2-row1	0.68727	0.285
Var 60h NI row2-row1	1.27489	0.904
Time course 0hI-0hNI	1.0163	1
Time course 12hI-12hNI	1.03268	0.868
Time course 36hI-36hNI	0.97471	0.569
Time course 60hI-60hNI	0.3909	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)	1.13257	0.571
transgenic ySAMdc/azygous control (breaker)	1.00702	1
transgenic ySAMdc/azygous control (red)	1.66867	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.95832	0.143

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.32776	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	2.1156	0.096
Manapal/WT (break)	1.84883	0.13
Manapal/WT (red)	1.44453	0.222