Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.4.5.3

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.24429	0.858
27DAP/17DAP	1.24166	0.793
39DAP/27DAP	1.13172	0.618
41DAP/39DAP	0.97585	0.833
42DAP/41DAP	0.97362	1
43DAP/42DAP	0.97796	0.925
47DAP/43DAP	1.08077	0.943
52DAP/47DAP	1.27141	0.671
57DAP/52DAP	1.56185	0.76

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.30576	0.024
17DAP/reference	0.4087	0.008
27DAP/reference	0.54047	0.02
39DAP/reference	0.68362	0.047
41DAP/reference	0.63948	0.039
42DAP/reference	0.56731	0.001
43DAP/reference	0.85684	0.135
47DAP/reference	0.60939	0.001
52DAP/reference	0.61627	0.067
57DAP/reference	0.85463	0.068

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.80197	0.096
27DAP/17DAP	0.77049	0.172
39DAP/27DAP	1.732	0.046
41DAP/39DAP	1.77166	0.013
42DAP/41DAP	0.49532	0.013
43DAP/42DAP	1.54172	0.025
47DAP/43DAP	1.13591	0.593
52DAP/47DAP	2.54996	0.036
57DAP/52DAP	2.21302	0.029
57DAP/7DAP	1.78592	0.207

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.47519	0.06
17DAP/reference	0.55734	0.011
27DAP/reference	0.65903	0.01
39DAP/reference	0.46126	0.011
41DAP/reference	0.57915	0.016
42DAP/reference	0.55235	0.01
43DAP/reference	0.44588	0.012
47DAP/reference	0.52226	0.044
52DAP/reference	0.38855	0.011
57DAP/reference	0.27002	0.006

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.42439	0.006
17DAP/reference	0.40898	0.003
27DAP/reference	0.64811	0.047
39DAP/reference	0.49166	0.01
41DAP/reference	0.6543	0.027
42DAP/reference	0.71065	0.015
43DAP/reference	0.4611	0.002
47DAP/reference	0.62135	0.013
52DAP/reference	0.43557	0.004
57DAP/reference	0.51827	0.004

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.46794	0.025
17DAP/reference	0.67767	0.118
27DAP/reference	0.49309	0.034
39DAP/reference	0.41008	0.006
41DAP/reference	0.54656	0.031
42DAP/reference	0.59597	0.016
43DAP/reference	0.62414	0.019
47DAP/reference	0.51334	0.005
52DAP/reference	0.81485	0.232
57DAP/reference	0.69826	0.028

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.60505	0.945
26DAP/20DAP	0.85438	1
34DAP/26DAP	1.07372	1
51DAP/34DAP	0.99558	0.758
52DAP/51DAP	1.2205	0.588
53DAP/52DAP	1.2962	0.662
55DAP/53DAP	1.12148	0.656
57DAP/55DAP	0.80851	0.516
62DAP/57DAP	1.08498	1
68DAP/62DAP	1.30122	0.549
68DAP/14DAP	1.02603	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	12.6971	0.014

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.18389	0.017
Immature Eggplant/Mature Eggplant	N/A	N/A
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	N/A	N/A
1-1-2/M82	N/A	N/A
12-2/M82	N/A	N/A
12-4/M82	N/A	N/A
1-3/M82	N/A	N/A
2-1-1/M82	N/A	N/A
2-1/M82	N/A	N/A
2-6/M82	N/A	N/A
3-2/M82	N/A	N/A
4-1-1/M82	N/A	N/A
4-1/M82	N/A	N/A
4-3-2/M82	N/A	N/A
4-3/M82	N/A	N/A
5-3/M82	N/A	N/A
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	1.12183	0.493
IL2-6/WTpooled	0.97887
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.22467
IL12-4/WTpooled	1.32446
IL1-4/WTpooled	0.91689	0.699
WT/WTpooled	1.13413	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	1.71884	0.479

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.50052	0.692
DC3000/delta hrp 6h	N/A	N/A
DC3000/delta hrp 12h	N/A	N/A
DC3000/delta hrp 24h	1.07798	0.779

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	5.35254
DC3000 delta B/DC3000 delta AB	6.03738

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	N/A	N/A
Exp 36h	N/A	N/A
Exp 60h	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
self-self	0.976
Var 0h	0.95835	1
Var 12h I row2-row1	1.32563	0.204
Var 12h NI row2-row1	1.03167	1
Var 36h I row2-row1	1.07673	1
Var 36h NI row2-row1	1.38123	1
Var 60h I row2-row1	1.06279	1
Var 60h NI row2-row1	0.64148	0.292
Time course 0hI-0hNI	1.1049	0.662
Time course 12hI-12hNI	3.53242	0.004
Time course 36hI-36hNI	4.27837	0.004
Time course 60hI-60hNI	6.09622	0.008

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)	N/A	N/A
transgenic ySAMdc/azygous control (breaker)	2.58595	0.248
transgenic ySAMdc/azygous control (red)	1.2572	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.97334	0.136

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.82288	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	N/A	N/A
Manapal/WT (break)	1.14806	1
Manapal/WT (red)	N/A	N/A