Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.3.13.17

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.93529	0.627
27DAP/17DAP	0.97758	0.843
39DAP/27DAP	0.94289	0.663
41DAP/39DAP	1.43972	0.212
42DAP/41DAP	1.09953	0.929
43DAP/42DAP	0.93684	0.883
47DAP/43DAP	0.95246	0.779
52DAP/47DAP	1.30795	0.516
57DAP/52DAP	0.9665	0.957

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.9841	0.727
17DAP/reference	0.79644	0.009
27DAP/reference	0.80096	0.011
39DAP/reference	0.97199	0.75
41DAP/reference	0.86789	0.154
42DAP/reference	0.81151	0.003
43DAP/reference	0.84319	0.015
47DAP/reference	0.80038	0.008
52DAP/reference	0.82158	0.021
57DAP/reference	0.76525	0.008

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.94302	0.484
27DAP/17DAP	0.97695	0.878
39DAP/27DAP	1.06638	0.611
41DAP/39DAP	0.99222	1
42DAP/41DAP	1.02872	0.976
43DAP/42DAP	1.02756	0.699
47DAP/43DAP	1.03338	0.897
52DAP/47DAP	1.04513	0.844
57DAP/52DAP	0.94425	0.48
57DAP/7DAP	1.05748	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.73073	0.071
17DAP/reference	0.74108	0.011
27DAP/reference	0.73693	0.01
39DAP/reference	0.78159	0.011
41DAP/reference	0.92788	0.311
42DAP/reference	0.83217	0.01
43DAP/reference	0.69718	0.011
47DAP/reference	0.59899	0.04
52DAP/reference	0.70051	0.011
57DAP/reference	0.66696	0.006

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.56205	0.006
17DAP/reference	0.5787	0.004
27DAP/reference	0.78198	0.155
39DAP/reference	0.49705	0.016
41DAP/reference	0.69032	0.047
42DAP/reference	0.68229	0.108
43DAP/reference	0.61893	0.003
47DAP/reference	0.77628	0.012
52DAP/reference	0.51715	0.003
57DAP/reference	0.56666	0.002

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.76143	0.032
17DAP/reference	0.72376	0.097
27DAP/reference	0.72156	0.025
39DAP/reference	0.70932	0.006
41DAP/reference	0.67571	0.019
42DAP/reference	0.67701	0.014
43DAP/reference	0.67239	0.024
47DAP/reference	0.59857	0.004
52DAP/reference	0.56792	0.047
57DAP/reference	0.55375	0.016

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.01387	1
26DAP/20DAP	0.90738	1
34DAP/26DAP	0.95095	0.816
51DAP/34DAP	1.12319	0.339
52DAP/51DAP	0.99531	1
53DAP/52DAP	0.99695	0.96
55DAP/53DAP	1.07937	0.656
57DAP/55DAP	0.99656	0.927
62DAP/57DAP	0.99323	0.994
68DAP/62DAP	0.88681	0.609
68DAP/14DAP	1.01817	0.936

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.85725	0.224

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	1.16966	0.752
Immature Eggplant/Mature Eggplant	6.39521	0.116
Ripe Pepper/Ripe Tomato	0.50221
Mature Eggplant/Ripe Tomato	0.60511

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.04172	1
1-1-2/M82	0.95268	1
12-2/M82	1.11955	1
12-4/M82	0.949	1
1-3/M82	0.85529	0.378
2-1-1/M82	1.01968	1
2-1/M82	N/A	N/A
2-6/M82	0.96515	1
3-2/M82	0.99926	1
4-1-1/M82	1.02234	1
4-1/M82	0.86623	1
4-3-2/M82	0.86139	1
4-3/M82	0.90145	1
5-3/M82	1.06555	1
6-2/M82	1.03203	1
6-3/M82	1.02206	1
7-1/M82	0.99911
7-2/M82	1.03469	1
9-3-2/M82	0.84596	0.449

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	0.97812	1
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.0523	1
IL12-4/WTpooled	1.04941	0.785
IL1-4/WTpooled	1.05381
WT/WTpooled	0.95868	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	0.73155	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.01346	1
DC3000/delta hrp 6h	1.35888	0.857
DC3000/delta hrp 12h	0.85423	1
DC3000/delta hrp 24h	1.70436	0.04

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.36858	0.076
DC3000 delta B/DC3000 delta AB	1.25535	0.179

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	1.00361	1
Var 0h	1.04837	1
Var 12h I row2-row1	1.16479	0.22
Var 12h NI row2-row1	0.98297	1
Var 36h I row2-row1	1.13646	1
Var 36h NI row2-row1	0.90855	0.61
Var 60h I row2-row1	1.10963	1
Var 60h NI row2-row1	1.08232	1
Time course 0hI-0hNI	1.12775	0.662
Time course 12hI-12hNI	1.04686	0.746
Time course 36hI-36hNI	1.06239	0.248
Time course 60hI-60hNI	1.2335	0.115

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)	0.77244	0.249
transgenic ySAMdc/azygous control (breaker)	0.8951	1
transgenic ySAMdc/azygous control (red)	1.11858	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.01298	0.619

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.47629	0.223

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.03647	1
Manapal/WT (break)	0.25468	0.333
Manapal/WT (red)	0.86233	0.183