Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.3.10.11

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.93427	0.627
27DAP/17DAP	0.97859	1
39DAP/27DAP	1.00484	0.84
41DAP/39DAP	1.1849	0.545
42DAP/41DAP	1.20845	0.916
43DAP/42DAP	0.98494	0.932
47DAP/43DAP	0.91897	0.71
52DAP/47DAP	1.32148	0.493
57DAP/52DAP	0.89473	0.82

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.01899	0.994
17DAP/reference	0.92017	0.111
27DAP/reference	0.8869	0.083
39DAP/reference	1.17515	0.359
41DAP/reference	1.04938	0.516
42DAP/reference	0.92591	0.012
43DAP/reference	0.96803	0.653
47DAP/reference	0.8899	0.002
52DAP/reference	0.92803	0.172
57DAP/reference	0.90792	0.031

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.87721	0.402
27DAP/17DAP	0.95976	0.878
39DAP/27DAP	0.92574	0.382
41DAP/39DAP	0.93069	0.875
42DAP/41DAP	1.06707	0.582
43DAP/42DAP	1.05423	0.554
47DAP/43DAP	1.04774	0.827
52DAP/47DAP	1.042	0.883
57DAP/52DAP	0.89702	0.501
57DAP/7DAP	0.81583	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.88421	0.091
17DAP/reference	0.99733	0.693
27DAP/reference	0.99264	0.698
39DAP/reference	0.93259	0.056
41DAP/reference	0.96291	0.213
42DAP/reference	0.98015	0.371
43DAP/reference	0.94678	0.028
47DAP/reference	0.92213	0.101
52DAP/reference	0.9069	0.213
57DAP/reference	0.85417	0.01

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.05258	0.516
17DAP/reference	0.98186	0.561
27DAP/reference	1.01369	1
39DAP/reference	0.96595	0.306
41DAP/reference	0.891	0.105
42DAP/reference	0.91862	0.169
43DAP/reference	1.22431	0.059
47DAP/reference	0.96054	0.319
52DAP/reference	0.95814	0.156
57DAP/reference	1.18556	0.094

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.96249	0.183
17DAP/reference	0.99028	0.739
27DAP/reference	0.98051	0.416
39DAP/reference	0.99587	0.819
41DAP/reference	1.08304	0.692
42DAP/reference	1.03768	0.635
43DAP/reference	0.99166	0.685
47DAP/reference	1.04048	0.519
52DAP/reference	0.88365	0.142
57DAP/reference	0.95239	0.372

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.07419	0.966
26DAP/20DAP	0.92102	1
34DAP/26DAP	0.9606	0.94
51DAP/34DAP	1.06028	0.937
52DAP/51DAP	0.90287	1
53DAP/52DAP	1.00342	1
55DAP/53DAP	1.15205	0.782
57DAP/55DAP	0.97854	0.904
62DAP/57DAP	1.15242	0.393
68DAP/62DAP	0.87241	0.579
68DAP/14DAP	1.05651	0.785

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.90282	0.028

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.45175
Mature Green Tomato/Ripe Tomato	1.01857	1
Immature Eggplant/Mature Eggplant	1.71396	0.05
Ripe Pepper/Ripe Tomato	1.03615	1
Mature Eggplant/Ripe Tomato	1.4377	0.373

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.94269	0.944
1-1-2/M82	0.97571	1
12-2/M82	1.07232	1
12-4/M82	1.16134	1
1-3/M82	0.93661	0.378
2-1-1/M82	1.14945	0.366
2-1/M82	N/A	N/A
2-6/M82	1.02904	1
3-2/M82	0.96999
4-1-1/M82	0.99141	1
4-1/M82	0.95017	1
4-3-2/M82	0.96064	1
4-3/M82	0.88682
5-3/M82	0.86895	0.395
6-2/M82	0.96158
6-3/M82	1.08646	1
7-1/M82	1.06385
7-2/M82	0.91666	0.881
9-3-2/M82	0.97203	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.40501	0.493
IL2-6/WTpooled	0.98982	1
IL7-5/WTpooled	0.32465	0.483
IL7-3/WTpooled	1.03706	1
IL12-4/WTpooled	0.82264	0.71
IL1-4/WTpooled	0.63088	0.562
WT/WTpooled	0.99646	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	1.09071	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.05553	0.914
DC3000/delta hrp 6h	1.02028	1
DC3000/delta hrp 12h	1.24648	1
DC3000/delta hrp 24h	0.94562	0.607

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.12937	0.313
DC3000 delta B/DC3000 delta AB	1.08387	0.503

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.23945	1
Exp 36h	1.33355	0.693
Exp 60h	1.80785	0.221

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

hybridization	ratio	FDR (corrected p value)
self-self	1.01533	1
Var 0h	0.53488	0.263
Var 12h I row2-row1	1.00867	1
Var 12h NI row2-row1	0.97764	0.713
Var 36h I row2-row1	1.28005	0.908
Var 36h NI row2-row1	1.05763	1
Var 60h I row2-row1	0.95656	0.952
Var 60h NI row2-row1	0.87072	0.292
Time course 0hI-0hNI	1.00989	1
Time course 12hI-12hNI	1.0122	0.833
Time course 36hI-36hNI	1.09863	0.128
Time course 60hI-60hNI	1.58135	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)	0.91386	0.246
transgenic ySAMdc/azygous control (breaker)	0.57638	0.132
transgenic ySAMdc/azygous control (red)	0.91183	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.04242	0.04

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.78454	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.82126	1
Manapal/WT (break)	0.9684	1
Manapal/WT (red)	1.38679	0.222