Tomato Functional Genomics Database (TFGD)

Expression of 1-1-6.3.9.18

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.95536	0.713
27DAP/17DAP	0.83675	0.585
39DAP/27DAP	1.33595	0.876
41DAP/39DAP	0.9174	0.63
42DAP/41DAP	1.03709	1
43DAP/42DAP	1.42047	0.625
47DAP/43DAP	0.89926	0.625
52DAP/47DAP	1.24202	0.806
57DAP/52DAP	0.93292	0.936

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.26868	0.162
17DAP/reference	0.75778	0.06
27DAP/reference	0.98992	0.694
39DAP/reference	0.90833	0.228
41DAP/reference	0.79875	0.011
42DAP/reference	0.89164	0.022
43DAP/reference	0.78474	0.015
47DAP/reference	0.87046	0.148
52DAP/reference	1.05072	0.695
57DAP/reference	1.05422	0.802

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.21403	0.605
27DAP/17DAP	1.11104	0.686
39DAP/27DAP	1.32596	0.359
41DAP/39DAP	1.35849	0.59
42DAP/41DAP	1.0352	0.825
43DAP/42DAP	1.07221	0.513
47DAP/43DAP	0.77992	0.093
52DAP/47DAP	1.19026	0.669
57DAP/52DAP	1.41298	0.265
57DAP/7DAP	0.96522	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.65368	0.034
17DAP/reference	1.40641	0.07
27DAP/reference	1.04144	0.664
39DAP/reference	1.08828	0.314
41DAP/reference	1.64565	0.011
42DAP/reference	1.06843	0.686
43DAP/reference	0.94908	0.385
47DAP/reference	0.8861	0.066
52DAP/reference	0.88104	0.137
57DAP/reference	0.70176	0.007

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.81428	0.154
17DAP/reference	1.16576	0.12
27DAP/reference	0.94413	0.352
39DAP/reference	0.87902	0.147
41DAP/reference	1.20154	0.106
42DAP/reference	1.01975	1
43DAP/reference	0.95371	0.486
47DAP/reference	0.92273	0.201
52DAP/reference	1.08899	0.702
57DAP/reference	0.72057	0.063

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.41376	0.053
17DAP/reference	1.33035	0.224
27DAP/reference	0.9814	0.594
39DAP/reference	1.17839	0.032
41DAP/reference	1.03697	0.692
42DAP/reference	0.8693	0.108
43DAP/reference	0.79267	0.064
47DAP/reference	0.80243	0.06
52DAP/reference	1.64511	0.928
57DAP/reference	0.87883	0.304

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.01174	1
26DAP/20DAP	0.94026	1
34DAP/26DAP	1.14238	1
51DAP/34DAP	1.45032
52DAP/51DAP	2.05473	0.848
53DAP/52DAP	1.14802	0.797
55DAP/53DAP	1.32534	0.429
57DAP/55DAP	1.3054	0.826
62DAP/57DAP	1.12759	1
68DAP/62DAP	0.96717	0.834
68DAP/14DAP	1.21597	0.594

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.10093	1

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.6888
Mature Green Tomato/Ripe Tomato	1.39246	1
Immature Eggplant/Mature Eggplant	1.29039	0.051
Ripe Pepper/Ripe Tomato	0.77769
Mature Eggplant/Ripe Tomato	1.38181	0.373

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	0.96644	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	0.96321
4-3/M82	N/A	N/A
5-3/M82	1.01616
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	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.12611	0.493
IL2-6/WTpooled	0.84464	0.348
IL7-5/WTpooled	0.67306
IL7-3/WTpooled	1.12631	1
IL12-4/WTpooled	1.10785	0.673
IL1-4/WTpooled	0.88527	0.699
WT/WTpooled	1.04296	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	1.00347	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.21441	0.875
DC3000/delta hrp 6h	0.87931	0.95
DC3000/delta hrp 12h	1.02236	1
DC3000/delta hrp 24h	0.7907	0.186

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	1.08923	1
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	0.97688	1
Var 0h	0.61651	0.332
Var 12h I row2-row1	0.98666	1
Var 12h NI row2-row1	0.69722	1
Var 36h I row2-row1	0.92844	1
Var 36h NI row2-row1	0.64504	0.706
Var 60h I row2-row1	1.00284
Var 60h NI row2-row1	0.68022	0.932
Time course 0hI-0hNI	1.18601	0.799
Time course 12hI-12hNI	0.94181	0.738
Time course 36hI-36hNI	0.92164	0.179
Time course 60hI-60hNI	0.91375	0.319

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)	0.84186	0.309
transgenic ySAMdc/azygous control (breaker)	0.5833	0.129
transgenic ySAMdc/azygous control (red)	0.88121	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.96158	0.074

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.82106	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.76894	1
Manapal/WT (break)	0.75563	1
Manapal/WT (red)	1.01239	1