Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.3.3.16

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.95256	0.689
27DAP/17DAP	0.59496	0.035
39DAP/27DAP	0.78152	0.353
41DAP/39DAP	0.65536	0.058
42DAP/41DAP	0.93826	1
43DAP/42DAP	1.30068	0.402
47DAP/43DAP	0.81024	0.41
52DAP/47DAP	0.75809	0.42
57DAP/52DAP	0.94881	0.949

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.87423	0.188
17DAP/reference	1.00857	1
27DAP/reference	1.07003	0.457
39DAP/reference	0.92792	0.188
41DAP/reference	0.92806	0.434
42DAP/reference	1.11179	1
43DAP/reference	0.70049	0.17
47DAP/reference	0.8675	0.004
52DAP/reference	0.88664	0.371
57DAP/reference	N/A	N/A

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.24326	0.271
27DAP/17DAP	1.09943	0.9
39DAP/27DAP	0.64699	0.034
41DAP/39DAP	0.98635	0.934
42DAP/41DAP	1.10365	0.861
43DAP/42DAP	0.89761	0.157
47DAP/43DAP	0.90825	0.339
52DAP/47DAP	0.86379	0.321
57DAP/52DAP	0.92396	0.598
57DAP/7DAP	0.4985	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	2.19196	0.024
17DAP/reference	1.91322	0.006
27DAP/reference	1.25709	0.013
39DAP/reference	1.56931	0.006
41DAP/reference	1.37221	0.057
42DAP/reference	1.4504	0.014
43DAP/reference	1.73799	0.006
47DAP/reference	1.35579	0.083
52DAP/reference	1.40202	0.02
57DAP/reference	1.717	0.007

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.13711	0.538
17DAP/reference	1.06917	0.571
27DAP/reference	1.1062	0.86
39DAP/reference	0.97934	0.497
41DAP/reference	1.14167	0.301
42DAP/reference	1.10762	0.309
43DAP/reference	0.68495	0.02
47DAP/reference	0.90921	0.133
52DAP/reference	0.94021	0.22
57DAP/reference	0.74295	0.006

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	2.25486	0.018
17DAP/reference	1.56426	0.224
27DAP/reference	1.91407	0.014
39DAP/reference	1.66453	0.016
41DAP/reference	1.40748	0.038
42DAP/reference	1.29078	0.117
43DAP/reference	1.43203	0.05
47DAP/reference	1.1577	0.218
52DAP/reference	1.66108	0.072
57DAP/reference	1.4066	0.013

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.14708	0.966
26DAP/20DAP	1.3389	0.293
34DAP/26DAP	0.9107	0.653
51DAP/34DAP	0.71361	0.069
52DAP/51DAP	0.92558	1
53DAP/52DAP	0.77084	0.307
55DAP/53DAP	0.57657	0.022
57DAP/55DAP	0.88135	0.496
62DAP/57DAP	1.44996	0.217
68DAP/62DAP	1.61128	0.058
68DAP/14DAP	1.53322	0.108

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.77103	0.035

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.94963	0.058
Mature Green Tomato/Ripe Tomato	2.66041	0.015
Immature Eggplant/Mature Eggplant	0.75013	0.065
Ripe Pepper/Ripe Tomato	1.77563	1
Mature Eggplant/Ripe Tomato	3.73572	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.31399	0.574
1-1-2/M82	1.21586	1
12-2/M82	0.85452	0.955
12-4/M82	1.15327	1
1-3/M82	1.76108	1
2-1-1/M82	0.95319	1
2-1/M82	0.44732	0.322
2-6/M82	3.33934	0.329
3-2/M82	0.61838	0.752
4-1-1/M82	1.25421	1
4-1/M82	1.69947	1
4-3-2/M82	1.4229	0.241
4-3/M82	1.11952	1
5-3/M82	0.71479	0.642
6-2/M82	1.24636	1
6-3/M82	1.25465	1
7-1/M82	0.69895	0.509
7-2/M82	2.4128	0.385
9-3-2/M82	1.69876	0.191

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.60587	0.247
IL2-6/WTpooled	0.5457
IL7-5/WTpooled	1.35526
IL7-3/WTpooled	0.95952	1
IL12-4/WTpooled	0.99056	1
IL1-4/WTpooled	0.94364	0.699
WT/WTpooled	1.26769	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	0.91904	0.497

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.04181	0.921
DC3000/delta hrp 6h	0.96738	0.95
DC3000/delta hrp 12h	1.10084	1
DC3000/delta hrp 24h	0.45869	0.034

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.61029	0.025
DC3000 delta B/DC3000 delta AB	0.60789	0.021

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.93115	1
Exp 36h	0.89113	0.699
Exp 60h	0.79286	0.249

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

hybridization	ratio	FDR (corrected p value)
self-self	1.01087	1
Var 0h	0.97567	0.98
Var 12h I row2-row1	0.83757	0.357
Var 12h NI row2-row1	0.93322	0.713
Var 36h I row2-row1	0.91204	0.805
Var 36h NI row2-row1	1.2859	0.482
Var 60h I row2-row1	1.05115	1
Var 60h NI row2-row1	1.12597	1
Time course 0hI-0hNI	0.92832	0.433
Time course 12hI-12hNI	1.04187	0.754
Time course 36hI-36hNI	0.90133	0.15
Time course 60hI-60hNI	0.14275	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)	0.96909	0.428
transgenic ySAMdc/azygous control (breaker)	1.22124	1
transgenic ySAMdc/azygous control (red)	1.21548	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.00592	1

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.47757	0.239

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.77773	0.105
Manapal/WT (break)	1.85253	0.183
Manapal/WT (red)	2.05133	0.137