Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.1.20.2

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.06272	0.947
27DAP/17DAP	1.12982	0.866
39DAP/27DAP	0.81538	0.399
41DAP/39DAP	1.28325	0.386
42DAP/41DAP	0.89247	1
43DAP/42DAP	0.86856	0.743
47DAP/43DAP	1.82206	0.405
52DAP/47DAP	1.17199	0.861
57DAP/52DAP	0.91068	0.7

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.4616
17DAP/reference	N/A	N/A
27DAP/reference	0.49813
39DAP/reference	0.92789
41DAP/reference	N/A	N/A
42DAP/reference	1.20673
43DAP/reference	N/A	N/A
47DAP/reference	N/A	N/A
52DAP/reference	0.4165
57DAP/reference	0.46452

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.11853	0.947
27DAP/17DAP	1.37476	0.344
39DAP/27DAP	0.9877	0.852
41DAP/39DAP	1.38024	0.641
42DAP/41DAP	1.14036	0.795
43DAP/42DAP	1.17229	0.585
47DAP/43DAP	1.10846	0.699
52DAP/47DAP	0.8945	0.56
57DAP/52DAP	1.08439	0.622
57DAP/7DAP	1.43582	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.9917	0.682
17DAP/reference	0.95001	0.389
27DAP/reference	0.99736	0.698
39DAP/reference	0.64697	0.013
41DAP/reference	0.79428	0.086
42DAP/reference	0.95231	0.415
43DAP/reference	0.91183	0.202
47DAP/reference	0.95715	0.383
52DAP/reference	0.99751	0.621
57DAP/reference	0.88853	0.156

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.00541	1
17DAP/reference	0.79478	0.011
27DAP/reference	0.70764	0.005
39DAP/reference	0.85221	0.11
41DAP/reference	0.74276	0.018
42DAP/reference	2.67596	0.433
43DAP/reference	0.82221	0.095
47DAP/reference	0.7621
52DAP/reference	0.93933	0.156
57DAP/reference	0.96386	0.488

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.06026	0.918
17DAP/reference	0.98811	0.739
27DAP/reference	0.99988	0.763
39DAP/reference	1.07149	0.711
41DAP/reference	1.16064	0.108
42DAP/reference	0.99826	0.816
43DAP/reference	0.81367	0.348
47DAP/reference	0.92645	0.207
52DAP/reference	2.12111	0.186
57DAP/reference	0.98389	0.682

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.10576	0.966
26DAP/20DAP	1.12827	0.635
34DAP/26DAP	1.22492	1
51DAP/34DAP	1.18233	0.293
52DAP/51DAP	1.16788	0.534
53DAP/52DAP	1.12259	0.398
55DAP/53DAP	1.00495	0.908
57DAP/55DAP	1.06128	1
62DAP/57DAP	1.07515	0.8
68DAP/62DAP	0.9648	0.81
68DAP/14DAP	0.96947	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.29113	0.855

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.92107
Mature Green Tomato/Ripe Tomato	0.80523	0.066
Immature Eggplant/Mature Eggplant	1.61477	0.069
Ripe Pepper/Ripe Tomato	0.85366	1
Mature Eggplant/Ripe Tomato	1.01923	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.91366	0.883
1-1-2/M82	1.02329	1
12-2/M82	1.00567	1
12-4/M82	1.22089	1
1-3/M82	1.08928
2-1-1/M82	1.07538	1
2-1/M82	1.03787	0.345
2-6/M82	0.81382	1
3-2/M82	1.00552
4-1-1/M82	0.84833
4-1/M82	1.08662
4-3-2/M82	0.96205	1
4-3/M82	0.97338	1
5-3/M82	0.89857	1
6-2/M82	1.18727	1
6-3/M82	1.38119	1
7-1/M82	0.94658	1
7-2/M82	0.94214	0.881
9-3-2/M82	0.90535	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.95796	1
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	0.70495	1
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	0.49633
IL1-4/WTpooled	2.77307	1
WT/WTpooled	0.86028

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	0.95334	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.32505	0.921
DC3000/delta hrp 6h	0.89176	0.95
DC3000/delta hrp 12h	1.15751	1
DC3000/delta hrp 24h	1.02679	1

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.13088	1
DC3000 delta B/DC3000 delta AB	0.91558

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.9084	1
Exp 36h	N/A	N/A
Exp 60h	1.00174	1

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

hybridization	ratio	FDR (corrected p value)
self-self	1.03221	1
Var 0h	N/A	N/A
Var 12h I row2-row1	0.99973	1
Var 12h NI row2-row1	0.97829	0.906
Var 36h I row2-row1	1.17085	1
Var 36h NI row2-row1	1.05979	1
Var 60h I row2-row1	0.86477	0.285
Var 60h NI row2-row1	1.02302	1
Time course 0hI-0hNI	1.0226	0.852
Time course 12hI-12hNI	1.00241	1
Time course 36hI-36hNI	1.29027	0.013
Time course 60hI-60hNI	4.03545	0.011

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)	1.06981	0.654
transgenic ySAMdc/azygous control (breaker)	0.8761	0.173
transgenic ySAMdc/azygous control (red)	0.96219	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.83539	1
Manapal/WT (break)	0.82441	1
Manapal/WT (red)	0.70514	0.184