Tomato Functional Genomics Database (TFGD)

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Expression of 1-1-5.1.17.18

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.30429	0.359
27DAP/17DAP	0.87624	0.708
39DAP/27DAP	1.07584	0.876
41DAP/39DAP	0.63749	0.06
42DAP/41DAP	1.08478	0.967
43DAP/42DAP	1.31964	0.409
47DAP/43DAP	1.17045	0.497
52DAP/47DAP	0.77594	0.436
57DAP/52DAP	0.79433	0.666

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.2254	0.139
17DAP/reference	0.95116	0.298
27DAP/reference	0.98184	0.683
39DAP/reference	0.92624	0.267
41DAP/reference	0.9851	0.814
42DAP/reference	1.14762	0.035
43DAP/reference	1.29137	0.095
47DAP/reference	1.7524	0.001
52DAP/reference	1.55756	0.011
57DAP/reference	1.34611	0.043

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.57698	0.036
27DAP/17DAP	0.96365	0.854
39DAP/27DAP	0.74116	0.058
41DAP/39DAP	0.86435	0.465
42DAP/41DAP	0.97812	0.774
43DAP/42DAP	1.0451	0.585
47DAP/43DAP	0.93244	0.534
52DAP/47DAP	0.86075	0.366
57DAP/52DAP	0.85232	0.272
57DAP/7DAP	0.53553	0.219

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.9175	0.224
17DAP/reference	0.90501	0.167
27DAP/reference	1.07699	0.301
39DAP/reference	0.98851	0.474
41DAP/reference	0.83066	0.139
42DAP/reference	0.84919	0.123
43DAP/reference	1.05009	0.974
47DAP/reference	1.10986	0.595
52DAP/reference	0.72737	0.012
57DAP/reference	0.77179	0.008

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.39985	0.404
17DAP/reference	0.94976	0.487
27DAP/reference	1.08026	0.552
39DAP/reference	1.19244	0.03
41DAP/reference	1.11993	0.48
42DAP/reference	1.07868	0.621
43DAP/reference	1.04005	0.846
47DAP/reference	0.9606	0.328
52DAP/reference	1.13924	0.667
57DAP/reference	1.19399	0.244

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.04722	0.631
17DAP/reference	1.02129	0.886
27DAP/reference	0.90252	0.23
39DAP/reference	0.90868	0.028
41DAP/reference	1.00104	0.682
42DAP/reference	1.08855	0.907
43DAP/reference	1.34367	0.142
47DAP/reference	1.3383	0.006
52DAP/reference	1.44492	0.509
57DAP/reference	1.54676	0.038

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.19142	0.966
26DAP/20DAP	0.91459	1
34DAP/26DAP	1.3061	1
51DAP/34DAP	0.62327	0.071
52DAP/51DAP	0.92691	1
53DAP/52DAP	0.80263	0.06
55DAP/53DAP	0.80141	0.077
57DAP/55DAP	1.34901	0.492
62DAP/57DAP	0.64619	0.162
68DAP/62DAP	0.97301	0.834
68DAP/14DAP	1.45906	N/A

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.77527	0.024

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.91512	0.491
Mature Green Tomato/Ripe Tomato	1.9189	0.03
Immature Eggplant/Mature Eggplant	2.24411	0.05
Ripe Pepper/Ripe Tomato	1.55359	0.258
Mature Eggplant/Ripe Tomato	1.56628	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	N/A	N/A
12-2/M82	N/A	N/A
12-4/M82	1.37924	1
1-3/M82	N/A	N/A
2-1-1/M82	N/A	N/A
2-1/M82	N/A	N/A
2-6/M82	N/A	N/A
3-2/M82	N/A	N/A
4-1-1/M82	N/A	N/A
4-1/M82	N/A	N/A
4-3-2/M82	1.48642	N/A
4-3/M82	1.06903	N/A
5-3/M82	1.10319	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	N/A	N/A
9-3-2/M82	1.87105	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.35058	0.243
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	0.61983	1
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	N/A	N/A
IL1-4/WTpooled	0.72957	0.338
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	1.05808	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.95056	1
DC3000/delta hrp 6h	0.80312	0.95
DC3000/delta hrp 12h	1.00187	1
DC3000/delta hrp 24h	1.20326	0.336

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.68215	0.023
DC3000 delta B/DC3000 delta AB	0.70934	0.021

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.03818	1
Exp 36h	1.04106	1
Exp 60h	1.44657	0.206

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

hybridization	ratio	FDR (corrected p value)
self-self	0.99051	1
Var 0h	0.93226	1
Var 12h I row2-row1	0.80488	0.338
Var 12h NI row2-row1	0.91082	0.627
Var 36h I row2-row1	1.02923	1
Var 36h NI row2-row1	1.27417	0.276
Var 60h I row2-row1	1.04843	1
Var 60h NI row2-row1	0.99158	1
Time course 0hI-0hNI	0.99141	1
Time course 12hI-12hNI	0.98398	0.889
Time course 36hI-36hNI	0.94343	0.302
Time course 60hI-60hNI	0.16886	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)	0.97828	0.722
transgenic ySAMdc/azygous control (breaker)	0.73629	0.15
transgenic ySAMdc/azygous control (red)	1.15323	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.77521	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.50101	0.093
Manapal/WT (break)	1.62123	0.381
Manapal/WT (red)	0.77448	0.607