Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.2.2.16

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.749	0.119
27DAP/17DAP	0.77302	0.494
39DAP/27DAP	0.80457	0.522
41DAP/39DAP	0.8679	0.469
42DAP/41DAP	1.11616	0.938
43DAP/42DAP	1.21246	0.587
47DAP/43DAP	0.95042	0.729
52DAP/47DAP	0.54892	0.109
57DAP/52DAP	1.18586	0.963

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.97802	0.562
17DAP/reference	0.82203	0.018
27DAP/reference	0.84105	0.057
39DAP/reference	0.80747	0.018
41DAP/reference	0.79377	0.031
42DAP/reference	1.00411	0.707
43DAP/reference	0.88109	0.021
47DAP/reference	1.06918	0.254
52DAP/reference	1.06308	0.766
57DAP/reference	1.02721	1

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.22707	0.63
27DAP/17DAP	0.65588	0.137
39DAP/27DAP	0.68475	0.053
41DAP/39DAP	1.0217	0.896
42DAP/41DAP	1.16836	0.436
43DAP/42DAP	1.08655	0.664
47DAP/43DAP	1.08588	0.853
52DAP/47DAP	1.00907	0.941
57DAP/52DAP	0.95407	0.691
57DAP/7DAP	N/A	N/A

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.17486	0.157
17DAP/reference	1.20393	0.123
27DAP/reference	1.01882	1
39DAP/reference	1.30302	0.036
41DAP/reference	1.17912	0.171
42DAP/reference	1.4125	0.308
43DAP/reference	1.29535	0.637
47DAP/reference	1.32862	0.182
52DAP/reference	1.11931	0.684
57DAP/reference	1.19771	0.007

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.04641	0.712
17DAP/reference	0.98986	0.626
27DAP/reference	0.93754	0.352
39DAP/reference	1.01937	1
41DAP/reference	1.06256	0.944
42DAP/reference	0.98037	0.534
43DAP/reference	0.85801	0.162
47DAP/reference	0.87729	0.105
52DAP/reference	1.06533	0.559
57DAP/reference	0.79172	0.018

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.36344	0.045
17DAP/reference	1.12135	0.551
27DAP/reference	1.18237	0.164
39DAP/reference	1.26263	0.157
41DAP/reference	1.35261	0.022
42DAP/reference	1.19527	0.142
43DAP/reference	1.08721	0.679
47DAP/reference	1.17922	0.077
52DAP/reference	1.1627	0.247
57DAP/reference	1.41614	0.036

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.9657	1
26DAP/20DAP	0.99128	1
34DAP/26DAP	0.78189	0.21
51DAP/34DAP	1.31117	0.149
52DAP/51DAP	0.9385	1
53DAP/52DAP	0.57041	0.393
55DAP/53DAP	1.03717	0.908
57DAP/55DAP	0.92211	0.828
62DAP/57DAP	3.48167	0.8
68DAP/62DAP	1.94473	0.012
68DAP/14DAP	1.48194	0.049

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.86234	0.175

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.55507	0.115
Mature Green Tomato/Ripe Tomato	1.43626
Immature Eggplant/Mature Eggplant	0.70317	0.407
Ripe Pepper/Ripe Tomato	3.76263	0.256
Mature Eggplant/Ripe Tomato	1.3011	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	1.0641	0.977
12-2/M82	N/A	N/A
12-4/M82	0.56081
1-3/M82	N/A	N/A
2-1-1/M82	N/A	N/A
2-1/M82	1.13807
2-6/M82	1.07576
3-2/M82	1.07909
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	1.51108
6-2/M82	1.10934
6-3/M82	1.05817
7-1/M82	0.91511
7-2/M82	1.04767
9-3-2/M82	1.37846

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.81996	0.321
IL2-6/WTpooled	0.91378	0.473
IL7-5/WTpooled	1.28633	0.792
IL7-3/WTpooled	1.05816	1
IL12-4/WTpooled	0.91283	0.71
IL1-4/WTpooled	1.05574	1
WT/WTpooled	0.9458	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	0.84694	0.75

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.87518	0.868
DC3000/delta hrp 6h	1.03155	1
DC3000/delta hrp 12h	0.87874	1
DC3000/delta hrp 24h	0.67939	0.034

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	N/A	N/A
DC3000 delta B/DC3000 delta AB	0.52279	0.02

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.95059	0.328
Exp 36h	0.76082	0.41
Exp 60h	0.56906	0.259

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

hybridization	ratio	FDR (corrected p value)
self-self	0.99551	1
Var 0h	0.7577	1
Var 12h I row2-row1	0.78838	0.39
Var 12h NI row2-row1	0.99489	1
Var 36h I row2-row1	0.9602	0.805
Var 36h NI row2-row1	1.08059	1
Var 60h I row2-row1	0.93754	0.439
Var 60h NI row2-row1	1.06531	0.904
Time course 0hI-0hNI	0.92825	0.43
Time course 12hI-12hNI	0.94549	0.519
Time course 36hI-36hNI	0.8125	0.023
Time course 60hI-60hNI	0.27866	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)	1.28718	0.273
transgenic ySAMdc/azygous control (breaker)	1.49964	0.161
transgenic ySAMdc/azygous control (red)	1.10259	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.95523	0.122

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.37876	0.239

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	2.48005	0.086
Manapal/WT (break)	1.8823	0.13
Manapal/WT (red)	1.43256	0.15