Tomato Functional Genomics Database (TFGD)

Expression of 1-1-8.4.13.10

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.81403	0.272
27DAP/17DAP	5.07504	0.066
39DAP/27DAP	0.58433	0.399
41DAP/39DAP	0.8878	0.518
42DAP/41DAP	1.36006	0.825
43DAP/42DAP	0.99298	0.918
47DAP/43DAP	0.7313	0.251
52DAP/47DAP	2.48762	0.059
57DAP/52DAP	0.85383	0.85

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.18554	0.265
17DAP/reference	1.06833	0.412
27DAP/reference	1.07901	0.405
39DAP/reference	1.14605	0.079
41DAP/reference	1.05372	0.516
42DAP/reference	1.91389	0.001
43DAP/reference	1.02638	0.758
47DAP/reference	0.91002	0.05
52DAP/reference	1.05487	0.8
57DAP/reference	0.98625	0.61

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.27573	0.871
27DAP/17DAP	0.97433	0.854
39DAP/27DAP	0.91721	0.54
41DAP/39DAP	1.95974	0.06
42DAP/41DAP	0.55997	0.011
43DAP/42DAP	1.81942	0.028
47DAP/43DAP	0.91839	0.499
52DAP/47DAP	4.3538	0.033
57DAP/52DAP	12.3177	0.029
57DAP/7DAP	7.99301	0.249

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.85259	0.138
17DAP/reference	1.1145	0.028
27DAP/reference	1.16686	0.16
39DAP/reference	0.97149	0.411
41DAP/reference	1.12615	0.184
42DAP/reference	1.3354	0.076
43DAP/reference	2.17357	0.006
47DAP/reference	0.78653	0.079
52DAP/reference	0.88541	0.15
57DAP/reference	2.59308	0.004

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.01052	0.993
17DAP/reference	1.44467	0.01
27DAP/reference	1.10396	0.526
39DAP/reference	1.03497	0.783
41DAP/reference	2.73804	0.005
42DAP/reference	1.65498	0.007
43DAP/reference	1.59675	0.021
47DAP/reference	2.17734	0.008
52DAP/reference	1.2653	0.024
57DAP/reference	1.35592	0.066

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.8386	0.044
17DAP/reference	1.04967	0.412
27DAP/reference	1.58071	0.013
39DAP/reference	1.38606	0.005
41DAP/reference	1.14501	0.239
42DAP/reference	1.30201	0.07
43DAP/reference	1.74376	0.007
47DAP/reference	1.35315	0.187
52DAP/reference	1.69877	0.053
57DAP/reference	2.82962	0.008

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.99059	1
26DAP/20DAP	0.60994
34DAP/26DAP	1.00377	1
51DAP/34DAP	0.8179	0.703
52DAP/51DAP	0.86185	1
53DAP/52DAP	0.91664	0.604
55DAP/53DAP	1.11078	0.693
57DAP/55DAP	1.45648	0.393
62DAP/57DAP	0.86734	0.871
68DAP/62DAP	0.88861	0.747
68DAP/14DAP	1.74566

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.61141	0.028

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.16477	0.017
Immature Eggplant/Mature Eggplant	0.58816	0.067
Ripe Pepper/Ripe Tomato	0.03083	0.224
Mature Eggplant/Ripe Tomato	0.47757	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.96326	0.961
1-1-2/M82	0.9863	1
12-2/M82	1.31648	1
12-4/M82	1.43584
1-3/M82	0.92878	1
2-1-1/M82	N/A	N/A
2-1/M82	N/A	N/A
2-6/M82	0.89666	1
3-2/M82	1.06133	0.967
4-1-1/M82	0.92616	1
4-1/M82	1.67136
4-3-2/M82	0.8155
4-3/M82	1.0888	1
5-3/M82	0.82452	0.642
6-2/M82	0.79637	0.497
6-3/M82	0.91721	1
7-1/M82	0.96726	1
7-2/M82	0.83556	0.599
9-3-2/M82	0.81513

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.96202	1
IL2-6/WTpooled	0.90807	0.473
IL7-5/WTpooled	0.85814	1
IL7-3/WTpooled	1.0075	1
IL12-4/WTpooled	0.9717	1
IL1-4/WTpooled	1.03491	1
WT/WTpooled	0.97037	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	1.1199	0.875
DC3000/delta hrp 6h	0.77119	0.947
DC3000/delta hrp 12h	1.03946	1
DC3000/delta hrp 24h	0.98561	0.966

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	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	0.97616	1
Var 0h	1.08724	0.936
Var 12h I row2-row1	1.31622	0.473
Var 12h NI row2-row1	1.00262	1
Var 36h I row2-row1	1.09219	0.742
Var 36h NI row2-row1	1.15055
Var 60h I row2-row1	0.90724	0.952
Var 60h NI row2-row1	1.14352	0.904
Time course 0hI-0hNI	1.13135	0.227
Time course 12hI-12hNI	0.8426	0.061
Time course 36hI-36hNI	1.13589	0.015
Time course 60hI-60hNI	1.56845	0.013

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)	1.8205	0.431
transgenic ySAMdc/azygous control (breaker)	0.25824	0.142
transgenic ySAMdc/azygous control (red)	1.53368	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.99131	0.431

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.28427	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.90968	1
Manapal/WT (break)	0.47959	0.333
Manapal/WT (red)	0.85423	0.503