Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.4.4.20

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.97376	0.779
27DAP/17DAP	1.41957	0.864
39DAP/27DAP	1.05318	1
41DAP/39DAP	0.84361	0.49
42DAP/41DAP	0.84254	0.774
43DAP/42DAP	1.05282	1
47DAP/43DAP	1.25567	0.809
52DAP/47DAP	0.73829	0.377
57DAP/52DAP	0.99988	0.992

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.08453	0.662
17DAP/reference	0.9858	0.858
27DAP/reference	0.94812	0.406
39DAP/reference	0.83781	0.141
41DAP/reference	0.97416	0.814
42DAP/reference	1.09304	0.609
43DAP/reference	0.85957
47DAP/reference	1.09476	0.764
52DAP/reference	0.90628	0.102
57DAP/reference	N/A	N/A

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.04222	1
27DAP/17DAP	0.90341	0.295
39DAP/27DAP	0.60498	0.029
41DAP/39DAP	0.71593	0.42
42DAP/41DAP	0.92222	0.61
43DAP/42DAP	0.82692	0.383
47DAP/43DAP	1.0951	0.963
52DAP/47DAP	0.59219
57DAP/52DAP	0.75851	0.531
57DAP/7DAP	0.54954	0.186

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.48572	0.039
17DAP/reference	1.17372	0.147
27DAP/reference	1.10726	0.551
39DAP/reference	0.99992	0.745
41DAP/reference	0.93541	0.394
42DAP/reference	1.04406	0.686
43DAP/reference	1.04793	1
47DAP/reference	0.99829	1
52DAP/reference	0.97949	0.523
57DAP/reference	0.87652	0.071

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.05777	0.794
17DAP/reference	1.0146	0.898
27DAP/reference	1.06301	0.781
39DAP/reference	1.03068	1
41DAP/reference	0.8705	0.133
42DAP/reference	0.82618	0.15
43DAP/reference	1.03899	0.814
47DAP/reference	0.94014	0.253
52DAP/reference	0.95161	0.351
57DAP/reference	0.93093	0.519

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.50359	0.019
17DAP/reference	1.26468	0.169
27DAP/reference	1.20103	0.029
39DAP/reference	1.19161	0.211
41DAP/reference	1.08458	0.916
42DAP/reference	1.0953	0.51
43DAP/reference	1.07147	0.515
47DAP/reference	1.11456	0.372
52DAP/reference	1.09192	0.609
57DAP/reference	1.9154	0.044

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.42834	0.966
26DAP/20DAP	1.03007
34DAP/26DAP	1.72412	1
51DAP/34DAP	1.15808	0.118
52DAP/51DAP	0.56604
53DAP/52DAP	1.18419	0.917
55DAP/53DAP	0.88841	0.709
57DAP/55DAP	1.13684	1
62DAP/57DAP	0.98515	1
68DAP/62DAP	0.81623	0.505
68DAP/14DAP	0.73496	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	2.10702	0.162

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.78499	0.113
Mature Green Tomato/Ripe Tomato	3.13472	0.015
Immature Eggplant/Mature Eggplant	0.52841	0.063
Ripe Pepper/Ripe Tomato	4.12747	0.256
Mature Eggplant/Ripe Tomato	5.13189	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.20282	0.574
1-1-2/M82	1.07341	1
12-2/M82	0.93537	0.862
12-4/M82	0.67172
1-3/M82	1.53433
2-1-1/M82	0.64617
2-1/M82	N/A	N/A
2-6/M82	1.92302	0.425
3-2/M82	0.55522	0.752
4-1-1/M82	1.48531
4-1/M82	N/A	N/A
4-3-2/M82	N/A	N/A
4-3/M82	1.48709	0.268
5-3/M82	0.94769	1
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	0.91364
7-2/M82	1.42751
9-3-2/M82	1.26386

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.33944
IL2-6/WTpooled	0.80452	0.358
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.97003	1
IL12-4/WTpooled	1.00249	1
IL1-4/WTpooled	1.01352	1
WT/WTpooled	0.9918	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	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.91219	1
DC3000/delta hrp 6h	0.93899	0.95
DC3000/delta hrp 12h	1.24693	1
DC3000/delta hrp 24h	0.58162	0.037

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	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.96436	1
Exp 36h	0.85382	0.749
Exp 60h	0.8001	0.586

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)	1.00933	0.612
transgenic ySAMdc/azygous control (breaker)	1.05408	1
transgenic ySAMdc/azygous control (red)	1.73077	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.89344	0.038

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	2.52119	0.222

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	3.75805	0.083
Manapal/WT (break)	2.99022	0.123
Manapal/WT (red)	2.72078	0.126