Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.4.4.15

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.87661	0.413
27DAP/17DAP	0.9024	0.822
39DAP/27DAP	1.00393	0.782
41DAP/39DAP	1.06491	0.511
42DAP/41DAP	1.13845	0.898
43DAP/42DAP	0.90275	0.7
47DAP/43DAP	1.00749	0.926
52DAP/47DAP	0.96688	0.779
57DAP/52DAP	0.96917	0.957

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.08956	1
17DAP/reference	0.64664	0.097
27DAP/reference	1.13569	0.735
39DAP/reference	0.69921	0.1
41DAP/reference	0.599	0.114
42DAP/reference	1.34264	0.398
43DAP/reference	1.47224	0.007
47DAP/reference	1.6108	0.015
52DAP/reference	2.41966	0.007
57DAP/reference	2.61245	0.008

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.0754	0.934
27DAP/17DAP	0.78786	0.179
39DAP/27DAP	0.8004	0.419
41DAP/39DAP	1.13411	0.362
42DAP/41DAP	0.9373	0.579
43DAP/42DAP	0.76326	0.089
47DAP/43DAP	0.94304	0.75
52DAP/47DAP	1.24412	0.519
57DAP/52DAP	1.416	0.256
57DAP/7DAP	2.85059	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.52211	0.039
17DAP/reference	1.11479	0.015
27DAP/reference	1.14297	0.02
39DAP/reference	1.45854	0.006
41DAP/reference	1.43375	0.019
42DAP/reference	1.96325	0.006
43DAP/reference	1.64683	0.008
47DAP/reference	1.53759	0.045
52DAP/reference	1.45967	0.011
57DAP/reference	1.21343	0.014

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.77638	0.268
17DAP/reference	0.54885	0.012
27DAP/reference	1.00989	0.663
39DAP/reference	1.52663	0.324
41DAP/reference	1.88161	0.005
42DAP/reference	1.4143	0.008
43DAP/reference	0.70736	0.009
47DAP/reference	1.38224	0.008
52DAP/reference	0.89095	0.043
57DAP/reference	0.45037

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.23173	0.044
17DAP/reference	0.90032	0.146
27DAP/reference	1.03348	0.749
39DAP/reference	1.25384	0.043
41DAP/reference	1.07341	0.306
42DAP/reference	1.47304	0.049
43DAP/reference	1.55674	0.037
47DAP/reference	1.13793	0.339
52DAP/reference	1.48735	0.067
57DAP/reference	4.46208	0.009

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.91956	1
26DAP/20DAP	1.23874	1
34DAP/26DAP	0.97389	0.988
51DAP/34DAP	1.42368	0.055
52DAP/51DAP	3.07936	0.126
53DAP/52DAP	0.87019	0.307
55DAP/53DAP	0.96497	0.775
57DAP/55DAP	1.00477	0.854
62DAP/57DAP	1.19986	0.622
68DAP/62DAP	0.85653
68DAP/14DAP	1.79954	0.041

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.33804	0.057

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.80338	0.312
Mature Green Tomato/Ripe Tomato	1.04882	0.774
Immature Eggplant/Mature Eggplant	0.71654	0.086
Ripe Pepper/Ripe Tomato	1.14657	0.256
Mature Eggplant/Ripe Tomato	0.88723	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.9955
1-1-2/M82	1.70474	1
12-2/M82	0.79522
12-4/M82	0.8424	0.33
1-3/M82	0.87725
2-1-1/M82	1.05137
2-1/M82	0.72812
2-6/M82	0.97494
3-2/M82	1.57118	0.463
4-1-1/M82	0.90402
4-1/M82	N/A	N/A
4-3-2/M82	1.15287
4-3/M82	1.13228
5-3/M82	0.97652	1
6-2/M82	1.05556
6-3/M82	0.80484
7-1/M82	0.81272
7-2/M82	0.86875	0.434
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.89933	0.247
IL2-6/WTpooled	1.20352	0.788
IL7-5/WTpooled	0.87482	1
IL7-3/WTpooled	0.69046	0.31
IL12-4/WTpooled	1.03082	1
IL1-4/WTpooled	0.95335	1
WT/WTpooled	1.02059	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	1.14259	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.06193	0.921
DC3000/delta hrp 6h	1.09278	1
DC3000/delta hrp 12h	1.03554	1
DC3000/delta hrp 24h	1.08727	0.483

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	0.72489

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.79323	1
Exp 36h	1.22902	0.693
Exp 60h	1.27413	0.563

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

hybridization	ratio	FDR (corrected p value)
self-self	N/A	N/A
Var 0h	N/A	N/A
Var 12h I row2-row1	N/A	N/A
Var 12h NI row2-row1	N/A	N/A
Var 36h I row2-row1	N/A	N/A
Var 36h NI row2-row1	N/A	N/A
Var 60h I row2-row1	N/A	N/A
Var 60h NI row2-row1	N/A	N/A
Time course 0hI-0hNI	N/A	N/A
Time course 12hI-12hNI	N/A	N/A
Time course 36hI-36hNI	N/A	N/A
Time course 60hI-60hNI	N/A	N/A

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)	1.16519	0.272
transgenic ySAMdc/azygous control (breaker)	1.21985	0.248
transgenic ySAMdc/azygous control (red)	1.04754	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.01886	0.525

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.85604	0.255

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.09648	1
Manapal/WT (break)	1.07331	1
Manapal/WT (red)	0.80547	0.181