Tomato Functional Genomics Database (TFGD)

Expression of 1-1-5.2.10.13

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.06765	0.932
27DAP/17DAP	0.68205	0.099
39DAP/27DAP	0.78486	0.482
41DAP/39DAP	0.91784	0.641
42DAP/41DAP	0.98594	1
43DAP/42DAP	1.1007	1
47DAP/43DAP	0.9729	0.847
52DAP/47DAP	0.98991	0.889
57DAP/52DAP	1.06998	0.964

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.69191	0.066
17DAP/reference	0.52536	0.013
27DAP/reference	0.44098	0.013
39DAP/reference	0.50246	0.044
41DAP/reference	0.26411	0.008
42DAP/reference	0.36146	0.001
43DAP/reference	0.27529	0.013
47DAP/reference	0.2242	0.001
52DAP/reference	0.21471	0.012
57DAP/reference	0.3104	0.006

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.6868	0.076
27DAP/17DAP	0.77453	0.295
39DAP/27DAP	0.33471	0.029
41DAP/39DAP	1.44134	0.058
42DAP/41DAP	0.78731	0.021
43DAP/42DAP	0.51049	0.022
47DAP/43DAP	0.9401	0.712
52DAP/47DAP	0.93069	0.729
57DAP/52DAP	0.91041	0.528
57DAP/7DAP	0.20267	0.219

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.02782	1
17DAP/reference	0.73145	0.011
27DAP/reference	0.44997	0.01
39DAP/reference	0.38927	0.011
41DAP/reference	0.30204	0.009
42DAP/reference	0.26219	0.01
43DAP/reference	0.1949	0.009
47DAP/reference	0.23607	0.027
52DAP/reference	0.26933	0.009
57DAP/reference	0.28343	0.006

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.46067	0.008
17DAP/reference	0.48019	0.015
27DAP/reference	0.63798	0.071
39DAP/reference	0.30367	0.008
41DAP/reference	0.39108	0.005
42DAP/reference	0.38542	0.011
43DAP/reference	0.17597	0.001
47DAP/reference	0.30853	0.009
52DAP/reference	0.19582	0.003
57DAP/reference	0.10612	0.002

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	2.03838	0.015
17DAP/reference	1.85705	0.048
27DAP/reference	1.15983	0.325
39DAP/reference	0.86882	0.163
41DAP/reference	0.65231	0.025
42DAP/reference	0.44247	0.015
43DAP/reference	0.46427	0.019
47DAP/reference	0.28441	0.004
52DAP/reference	0.25065	0.047
57DAP/reference	1.24065	0.682

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.0546	1
26DAP/20DAP	1.24121	0.409
34DAP/26DAP	0.75233	0.131
51DAP/34DAP	0.47033	0.049
52DAP/51DAP	1.01099	1
53DAP/52DAP	0.62608	0.049
55DAP/53DAP	0.78323	0.044
57DAP/55DAP	0.98614	0.911
62DAP/57DAP	1.30955	0.098
68DAP/62DAP	1.03084	1
68DAP/14DAP	0.35366	0.078

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.34208	0.02

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	3.20457	0.058
Mature Green Tomato/Ripe Tomato	7.25742	0.015
Immature Eggplant/Mature Eggplant	0.49378	0.062
Ripe Pepper/Ripe Tomato	22.8746	0.256
Mature Eggplant/Ripe Tomato	43.4365	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.87732	0.944
1-1-2/M82	0.87624	1
12-2/M82	1.00058
12-4/M82	1.25528	1
1-3/M82	0.86244
2-1-1/M82	N/A	N/A
2-1/M82	N/A	N/A
2-6/M82	1.0131	1
3-2/M82	N/A	N/A
4-1-1/M82	0.99052	1
4-1/M82	1.01278
4-3-2/M82	0.91186	1
4-3/M82	0.92475	0.72
5-3/M82	1.23915	1
6-2/M82	N/A	N/A
6-3/M82	1.07786
7-1/M82	N/A	N/A
7-2/M82	0.97074
9-3-2/M82	0.66739	0.449

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.3564
IL2-6/WTpooled	0.96973	1
IL7-5/WTpooled	0.62142
IL7-3/WTpooled	0.82757	0.418
IL12-4/WTpooled	0.93834	0.581
IL1-4/WTpooled	1.12324	1
WT/WTpooled	1.0397	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	1.00487	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.97211	1
DC3000/delta hrp 6h	1.02036	0.95
DC3000/delta hrp 12h	1.02527	1
DC3000/delta hrp 24h	0.97395	0.769

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.04524	0.333
DC3000 delta B/DC3000 delta AB	0.56164	0.03

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.07481	1
Exp 36h	1.05488	1
Exp 60h	0.95719	0.855

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

hybridization	ratio	FDR (corrected p value)
self-self	0.99588	1
Var 0h	1.26421	0.98
Var 12h I row2-row1	1.04585	0.272
Var 12h NI row2-row1	1.00878	1
Var 36h I row2-row1	1.1528	0.908
Var 36h NI row2-row1	0.99394	1
Var 60h I row2-row1	1.53603	0.562
Var 60h NI row2-row1	0.99495	1
Time course 0hI-0hNI	1.00846	1
Time course 12hI-12hNI	1.00455	0.892
Time course 36hI-36hNI	1.0113	0.881
Time course 60hI-60hNI	0.48308	0.011

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)	1.14819	0.748
transgenic ySAMdc/azygous control (breaker)	3.9009	0.162
transgenic ySAMdc/azygous control (red)	1.58841	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.52747	0.08

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.99716	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	30.1724	0.084
Manapal/WT (break)	14.3395	0.123
Manapal/WT (red)	3.83458	0.413