Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.2.12.15

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.96211	0.728
27DAP/17DAP	0.43143	0.027
39DAP/27DAP	0.68875	0.335
41DAP/39DAP	0.58797	0.045
42DAP/41DAP	0.77197	0.774
43DAP/42DAP	1.4065	0.736
47DAP/43DAP	0.31739	0.049
52DAP/47DAP	1.10986	0.906
57DAP/52DAP	1.01817	0.983

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.8199	0.125
17DAP/reference	0.5988	0.008
27DAP/reference	0.56725	0.013
39DAP/reference	0.53457	0.015
41DAP/reference	0.43425	0.008
42DAP/reference	0.46747	0.001
43DAP/reference	0.41379	0.013
47DAP/reference	0.37529	0.001
52DAP/reference	0.32624	0.012
57DAP/reference	0.42498	0.007

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.88447	0.036
27DAP/17DAP	0.67643	0.164
39DAP/27DAP	0.31397	0.029
41DAP/39DAP	1.65568	0.012
42DAP/41DAP	0.80439	0.06
43DAP/42DAP	0.47273	0.022
47DAP/43DAP	0.88488	0.319
52DAP/47DAP	1.06909	0.8
57DAP/52DAP	1.01953	0.81
57DAP/7DAP	0.18546	0.219

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.22947	0.065
17DAP/reference	0.95169	0.253
27DAP/reference	0.69174	0.01
39DAP/reference	0.48114	0.011
41DAP/reference	0.40691	0.009
42DAP/reference	0.52806	0.015
43DAP/reference	0.30565	0.009
47DAP/reference	0.30444	0.032
52DAP/reference	0.3704	0.011
57DAP/reference	0.4167	0.006

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.57704	0.009
17DAP/reference	0.62444	0.017
27DAP/reference	0.84413	0.22
39DAP/reference	0.47117	0.011
41DAP/reference	0.61413	0.009
42DAP/reference	0.52523	0.012
43DAP/reference	0.32541	0.002
47DAP/reference	0.44931	0.007
52DAP/reference	0.26206	0.003
57DAP/reference	0.22214	0.002

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	2.12779	0.015
17DAP/reference	2.02243	0.111
27DAP/reference	1.50999	0.025
39DAP/reference	1.20777	0.151
41DAP/reference	0.83968	0.058
42DAP/reference	0.6653	0.028
43DAP/reference	0.64611	0.017
47DAP/reference	0.36248	0.004
52DAP/reference	0.45265	0.047
57DAP/reference	1.4286	0.268

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.0012	1
26DAP/20DAP	1.10025	0.916
34DAP/26DAP	0.82757	0.129
51DAP/34DAP	0.40059	0.049
52DAP/51DAP	0.95738	1
53DAP/52DAP	0.5545	0.049
55DAP/53DAP	0.53843	0.019
57DAP/55DAP	0.9465	0.754
62DAP/57DAP	1.32285	0.217
68DAP/62DAP	0.9412	0.747
68DAP/14DAP	0.44002	0.121

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.30659	0.02

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.9327	0.058
Mature Green Tomato/Ripe Tomato	13.4125	0.015
Immature Eggplant/Mature Eggplant	0.61189	0.063
Ripe Pepper/Ripe Tomato	2.45704	1
Mature Eggplant/Ripe Tomato	4.32107	0.373

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.11899	1
1-1-2/M82	0.97298	1
12-2/M82	0.95735	0.955
12-4/M82	0.97759	1
1-3/M82	0.92459	0.378
2-1-1/M82	1.115	0.32
2-1/M82	1.16809	1
2-6/M82	1.05826	0.695
3-2/M82	0.98514
4-1-1/M82	1.05382	1
4-1/M82	0.96709
4-3-2/M82	1.34803
4-3/M82	1.15811	1
5-3/M82	1.05057	1
6-2/M82	1.1063	1
6-3/M82	1.0172	1
7-1/M82	1.00131	1
7-2/M82	1.077	1
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	0.8876
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.85467
IL12-4/WTpooled	0.82571	0.71
IL1-4/WTpooled	1.65592	1
WT/WTpooled	1.13938	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	1.004	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.02511
DC3000/delta hrp 6h	0.99649	0.95
DC3000/delta hrp 12h	1.02767	1
DC3000/delta hrp 24h	0.96961	0.782

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.73899	0.023
DC3000 delta B/DC3000 delta AB	0.64485	0.093

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.00593	1
Exp 36h	1.03263	1
Exp 60h	1.11897	0.563

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

hybridization	ratio	FDR (corrected p value)
self-self	1.0444	1
Var 0h	1.26515	0.311
Var 12h I row2-row1	1.01373	1
Var 12h NI row2-row1	1.04129	1
Var 36h I row2-row1	1.01486	1
Var 36h NI row2-row1	0.93257	0.645
Var 60h I row2-row1	1.49464	0.562
Var 60h NI row2-row1	0.96477	1
Time course 0hI-0hNI	1.02435	0.867
Time course 12hI-12hNI	0.99427	0.994
Time course 36hI-36hNI	1.03913	0.722
Time course 60hI-60hNI	0.50324	0.009

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)	1.18661	0.482
transgenic ySAMdc/azygous control (breaker)	1.6981	0.172
transgenic ySAMdc/azygous control (red)	1.00309	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.55039	0.083

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.11983	0.277

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	11.1742	0.096
Manapal/WT (break)	4.14908	0.123
Manapal/WT (red)	0.86911	0.315