Tomato Functional Genomics Database (TFGD)

Expression of 1-1-5.1.7.12

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.03508	0.904
27DAP/17DAP	0.92753	0.869
39DAP/27DAP	1.07535	0.845
41DAP/39DAP	0.93601	0.711
42DAP/41DAP	0.98641	1
43DAP/42DAP	1.00786	1
47DAP/43DAP	1.06649	0.715
52DAP/47DAP	0.94334	0.818
57DAP/52DAP	1.14745	0.952

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.0166	0.928
17DAP/reference	0.91561	0.079
27DAP/reference	1.00132	0.923
39DAP/reference	0.93203	0.194
41DAP/reference	0.92118	0.049
42DAP/reference	0.95488	0.067
43DAP/reference	0.98466	0.763
47DAP/reference	0.99659	0.674
52DAP/reference	0.9994	0.709
57DAP/reference	1.10677	0.018

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.94767	0.484
27DAP/17DAP	0.9852	0.782
39DAP/27DAP	0.96643	0.703
41DAP/39DAP	1.01559	1
42DAP/41DAP	1.20377	0.763
43DAP/42DAP	1.10642	0.122
47DAP/43DAP	0.96452	0.774
52DAP/47DAP	0.98975	0.941
57DAP/52DAP	0.89254	0.209
57DAP/7DAP	0.90311	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.9591	0.157
17DAP/reference	0.95922	0.338
27DAP/reference	0.95869	0.125
39DAP/reference	0.93963	0.034
41DAP/reference	0.97428	0.203
42DAP/reference	1.04077	0.405
43DAP/reference	0.92008	0.044
47DAP/reference	0.91223	0.057
52DAP/reference	0.95647	0.126
57DAP/reference	0.88348	0.014

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.90932	0.197
17DAP/reference	0.91253	0.176
27DAP/reference	1.06302	0.726
39DAP/reference	1.00988	0.769
41DAP/reference	1.009	1
42DAP/reference	0.89961	0.15
43DAP/reference	0.95334	0.336
47DAP/reference	0.93061	0.137
52DAP/reference	0.95049	0.051
57DAP/reference	0.91438	0.116

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.92511	0.055
17DAP/reference	0.95214	0.499
27DAP/reference	0.97841	0.624
39DAP/reference	0.95716	0.101
41DAP/reference	0.99838	0.826
42DAP/reference	0.99951	1
43DAP/reference	0.98454	0.66
47DAP/reference	0.94948	0.231
52DAP/reference	1.04267	0.759
57DAP/reference	1.43656	0.017

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.01593	0.966
26DAP/20DAP	0.8349	0.512
34DAP/26DAP	1.02973	1
51DAP/34DAP	0.98482	0.883
52DAP/51DAP	1.03735	0.708
53DAP/52DAP	0.87817	0.202
55DAP/53DAP	1.11689
57DAP/55DAP	1.14102	0.71
62DAP/57DAP	0.93119	1
68DAP/62DAP	1.02323	0.939
68DAP/14DAP	0.89476

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.74372	0.05

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.01481	1
Mature Green Tomato/Ripe Tomato	0.8991	0.446
Immature Eggplant/Mature Eggplant	1.04532	0.528
Ripe Pepper/Ripe Tomato	1.00714	1
Mature Eggplant/Ripe Tomato	1.3312	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.93118	0.944
1-1-2/M82	1.01154	1
12-2/M82	0.81544	0.955
12-4/M82	1.06006	1
1-3/M82	0.95241	0.501
2-1-1/M82	0.9331	0.92
2-1/M82	0.86567	0.74
2-6/M82	0.93958	1
3-2/M82	1.02132	0.967
4-1-1/M82	0.99856	1
4-1/M82	0.95991
4-3-2/M82	0.92734	1
4-3/M82	0.91082	0.72
5-3/M82	1.01625	1
6-2/M82	0.96993	1
6-3/M82	1.02312	1
7-1/M82	1.05873	0.598
7-2/M82	0.96861	1
9-3-2/M82	0.91593	0.449

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.98763	1
IL2-6/WTpooled	0.96763	1
IL7-5/WTpooled	0.80973	1
IL7-3/WTpooled	1.17379
IL12-4/WTpooled	0.88946	0.71
IL1-4/WTpooled	1.04666	1
WT/WTpooled	1.01886	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	1.20407	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.90291	1
DC3000/delta hrp 6h	0.99673	0.95
DC3000/delta hrp 12h	1.03851	1
DC3000/delta hrp 24h	1.01877	0.779

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.75267	0.031
DC3000 delta B/DC3000 delta AB	0.79472	0.025

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	0.99848	1
Var 0h	1.00415	1
Var 12h I row2-row1	0.82498	0.467
Var 12h NI row2-row1	0.94374	0.82
Var 36h I row2-row1	1.10977	0.305
Var 36h NI row2-row1	1.14806	0.482
Var 60h I row2-row1	1.10932	0.562
Var 60h NI row2-row1	0.97904	1
Time course 0hI-0hNI	0.99412	1
Time course 12hI-12hNI	0.92394	0.238
Time course 36hI-36hNI	0.81661	0.029
Time course 60hI-60hNI	0.26649	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)	0.88807	0.377
transgenic ySAMdc/azygous control (breaker)	0.82537	0.142
transgenic ySAMdc/azygous control (red)	1.08492	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.01747	0.471

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.19668	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.77165	1
Manapal/WT (break)	0.91324	0.333
Manapal/WT (red)	1.45564	0.413