Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.3.1.12

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.94796	0.689
27DAP/17DAP	0.85199	0.558
39DAP/27DAP	0.80602	0.397
41DAP/39DAP	1.01652	0.925
42DAP/41DAP	1.09898	0.954
43DAP/42DAP	0.92343	0.801
47DAP/43DAP	0.93127	0.746
52DAP/47DAP	0.96582	0.789
57DAP/52DAP	1.03667	1

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.99916	0.787
17DAP/reference	1.05424	0.117
27DAP/reference	1.01391	0.771
39DAP/reference	1.02543	0.27
41DAP/reference	0.98672	0.814
42DAP/reference	0.98162	0.326
43DAP/reference	1.05285	0.34
47DAP/reference	0.93477	0.127
52DAP/reference	0.9424	0.33
57DAP/reference	0.85424	0.131

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.31963	0.114
27DAP/17DAP	0.96658	0.821
39DAP/27DAP	0.76264	0.076
41DAP/39DAP	1.09303	0.623
42DAP/41DAP	0.91862	0.284
43DAP/42DAP	0.90974	0.082
47DAP/43DAP	0.94444	0.402
52DAP/47DAP	1.01011	0.991
57DAP/52DAP	0.91545	0.145
57DAP/7DAP	1.08324	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.85832	0.296
17DAP/reference	0.84696	0.015
27DAP/reference	0.82396	0.013
39DAP/reference	0.84778	0.049
41DAP/reference	0.86233	0.049
42DAP/reference	0.76576	0.01
43DAP/reference	0.75807	0.014
47DAP/reference	0.97961	0.671
52DAP/reference	0.7699	0.012
57DAP/reference	0.86972	0.031

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.96229	0.688
17DAP/reference	1.05235	0.484
27DAP/reference	1.04298	0.781
39DAP/reference	1.00368	0.769
41DAP/reference	1.03492	0.831
42DAP/reference	0.91894	0.042
43DAP/reference	1.05485	0.547
47DAP/reference	0.99504	0.678
52DAP/reference	1.012	0.747
57DAP/reference	1.00143	0.874

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.86364	0.119
17DAP/reference	1.05735	0.638
27DAP/reference	0.93773	0.397
39DAP/reference	0.82157	0.014
41DAP/reference	0.89672	0.417
42DAP/reference	0.93005	0.287
43DAP/reference	0.87766	0.032
47DAP/reference	1.12771	0.063
52DAP/reference	0.72172	0.131
57DAP/reference	0.98137	0.633

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.1268	0.678
26DAP/20DAP	1.00815	1
34DAP/26DAP	0.91201	0.394
51DAP/34DAP	0.77915	0.152
52DAP/51DAP	0.97657	1
53DAP/52DAP	0.9541	0.715
55DAP/53DAP	1.09696	0.656
57DAP/55DAP	0.91414	0.647
62DAP/57DAP	1.1135	0.057
68DAP/62DAP	0.87671	0.668
68DAP/14DAP	0.88637	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.8952	0.079

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.11498	0.417
Mature Green Tomato/Ripe Tomato	1.10447	1
Immature Eggplant/Mature Eggplant	0.74654	0.096
Ripe Pepper/Ripe Tomato	1.34338	1
Mature Eggplant/Ripe Tomato	0.90368	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.9681	0.883
1-1-2/M82	0.94824	1
12-2/M82	0.99827	1
12-4/M82	0.93679	1
1-3/M82	0.85272	0.441
2-1-1/M82	1.26422	0.457
2-1/M82	1.30927
2-6/M82	1.25842	0.505
3-2/M82	0.90451
4-1-1/M82	0.95602	1
4-1/M82	0.96183	0.737
4-3-2/M82	0.80844	0.698
4-3/M82	1.09217
5-3/M82	0.98733	1
6-2/M82	0.98966	1
6-3/M82	0.99039	1
7-1/M82	1.04468	1
7-2/M82	1.05138	1
9-3-2/M82	0.88211	0.449

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.69535	0.277
IL2-6/WTpooled	0.48752
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.16794	1
IL12-4/WTpooled	1.13712	0.785
IL1-4/WTpooled	3.78128
WT/WTpooled	1.2154	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	1.30771	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.01775	1
DC3000/delta hrp 6h	1.39106	0.582
DC3000/delta hrp 12h	0.95295	1
DC3000/delta hrp 24h	1.06647	0.438

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.61022	0.077
DC3000 delta B/DC3000 delta AB	0.4345	0.021

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.00212	1
Exp 36h	1.07057	1
Exp 60h	0.90803	0.664

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

hybridization	ratio	FDR (corrected p value)
self-self	1.08813	1
Var 0h	1.06729	0.98
Var 12h I row2-row1	0.89754	0.565
Var 12h NI row2-row1	1.03453	1
Var 36h I row2-row1	1.16319	1
Var 36h NI row2-row1	1.32525	1
Var 60h I row2-row1	1.41538	0.562
Var 60h NI row2-row1	1.06849	0.904
Time course 0hI-0hNI	0.98711	0.985
Time course 12hI-12hNI	0.96498	0.82
Time course 36hI-36hNI	0.94487	0.306
Time course 60hI-60hNI	0.21769	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)	1.07073	0.397
transgenic ySAMdc/azygous control (breaker)	1.01447	1
transgenic ySAMdc/azygous control (red)	0.92569	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.03546	0.287

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.20005	0.222

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.10117	0.307
Manapal/WT (break)	1.08382	1
Manapal/WT (red)	1.23033	0.164