Tomato Functional Genomics Database (TFGD)

Expression of 1-1-5.2.7.8

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.88415	0.413
27DAP/17DAP	0.95154	0.911
39DAP/27DAP	1.2717	1
41DAP/39DAP	1.21483	0.685
42DAP/41DAP	0.75026	0.774
43DAP/42DAP	0.918	0.874
47DAP/43DAP	1.16046	0.633
52DAP/47DAP	1.22355	0.667
57DAP/52DAP	1.04788	0.971

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.41756	0.02
17DAP/reference	0.90297	0.342
27DAP/reference	0.91054	0.314
39DAP/reference	0.85567	0.11
41DAP/reference	0.7417	0.018
42DAP/reference	1.05215	0.609
43DAP/reference	0.94649	0.429
47DAP/reference	1.09274	0.419
52DAP/reference	1.14534	0.302
57DAP/reference	1.09491	0.379

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.01316	0.899
27DAP/17DAP	1.0496	0.938
39DAP/27DAP	1.06723	0.793
41DAP/39DAP	0.89952	0.793
42DAP/41DAP	0.98563	0.772
43DAP/42DAP	0.92601	0.576
47DAP/43DAP	1.06637	0.822
52DAP/47DAP	1.30168	0.374
57DAP/52DAP	0.89292	0.476
57DAP/7DAP	0.93534

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.32282	0.038
17DAP/reference	1.13089	0.077
27DAP/reference	1.30201	0.049
39DAP/reference	1.16762	0.297
41DAP/reference	1.125	0.325
42DAP/reference	1.22199	0.405
43DAP/reference	1.13701	0.307
47DAP/reference	1.23873	0.035
52DAP/reference	1.2717	0.023
57DAP/reference	1.15706	0.011

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.97331	0.706
17DAP/reference	0.98694	0.626
27DAP/reference	1.40285	0.111
39DAP/reference	1.47398	0.08
41DAP/reference	1.72213	0.013
42DAP/reference	1.46085	0.024
43DAP/reference	1.02093	0.774
47DAP/reference	1.02674	0.77
52DAP/reference	0.95656	0.327
57DAP/reference	0.62551	0.011

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.23923	0.162
17DAP/reference	1.14321	0.578
27DAP/reference	1.1561	0.1
39DAP/reference	1.06438	0.39
41DAP/reference	1.17592	0.15
42DAP/reference	1.34645	0.045
43DAP/reference	1.78596	0.039
47DAP/reference	1.04482	1
52DAP/reference	1.84974	0.17
57DAP/reference	2.07759	0.009

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.03453	1
26DAP/20DAP	0.82573	1
34DAP/26DAP	1.91213
51DAP/34DAP	0.65847	0.112
52DAP/51DAP	1.12398	0.77
53DAP/52DAP	0.9592	0.835
55DAP/53DAP	1.15788	0.355
57DAP/55DAP	1.10138	0.902
62DAP/57DAP	1.53595	0.868
68DAP/62DAP	4.14574	0.017
68DAP/14DAP	3.44565	0.021

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.02577	1

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.32736	0.058
Mature Green Tomato/Ripe Tomato	1.04966	0.752
Immature Eggplant/Mature Eggplant	1.58611	0.063
Ripe Pepper/Ripe Tomato	0.56959	0.224
Mature Eggplant/Ripe Tomato	1.27031	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.9679	0.944
1-1-2/M82	N/A	N/A
12-2/M82	N/A	N/A
12-4/M82	0.98703	1
1-3/M82	1.07227
2-1-1/M82	N/A	N/A
2-1/M82	N/A	N/A
2-6/M82	1.20415	0.329
3-2/M82	0.78907
4-1-1/M82	N/A	N/A
4-1/M82	N/A	N/A
4-3-2/M82	1.21006
4-3/M82	N/A	N/A
5-3/M82	1.12119	1
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	1.04795	0.282
9-3-2/M82	0.74703

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	N/A	N/A
IL1-4/WTpooled	N/A	N/A
WT/WTpooled	N/A	N/A

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	1.10083	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.02325	0.921
DC3000/delta hrp 6h	0.9155	0.95
DC3000/delta hrp 12h	1.08391	1
DC3000/delta hrp 24h	0.89157	0.319

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	1.05387	0.703

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	0.98793	1
Var 0h	0.88445	1
Var 12h I row2-row1	0.93637	0.627
Var 12h NI row2-row1	0.87661	0.546
Var 36h I row2-row1	1.06744	1
Var 36h NI row2-row1	1.10155	1
Var 60h I row2-row1	1.03415	0.523
Var 60h NI row2-row1	0.97784	1
Time course 0hI-0hNI	1.01591	0.852
Time course 12hI-12hNI	0.96256	0.745
Time course 36hI-36hNI	0.88744	0.023
Time course 60hI-60hNI	0.57521	0.006

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)	1.36269	0.339
transgenic ySAMdc/azygous control (breaker)	0.43753	0.139
transgenic ySAMdc/azygous control (red)	1.11447	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.0326	0.723

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.61802	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.72093	1
Manapal/WT (break)	0.82539	0.333
Manapal/WT (red)	1.01606	1