Tomato Functional Genomics Database (TFGD)

Expression of 1-1-5.1.7.6

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.17526	0.523
27DAP/17DAP	1.04321	0.9
39DAP/27DAP	0.92265	0.608
41DAP/39DAP	1.07339	0.859
42DAP/41DAP	1.02583	1
43DAP/42DAP	0.99583	0.937
47DAP/43DAP	1.23167	0.49
52DAP/47DAP	0.86191	0.63
57DAP/52DAP	1.06992	0.952

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.77582	0.05
17DAP/reference	0.69969	0.007
27DAP/reference	0.93791	0.525
39DAP/reference	0.834	0.081
41DAP/reference	0.64311	0.008
42DAP/reference	0.80959	0.024
43DAP/reference	0.88995	0.148
47DAP/reference	0.95575	0.322
52DAP/reference	1.17153	0.02
57DAP/reference	1.22099	0.039

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.91932	0.299
27DAP/17DAP	1.00935	0.98
39DAP/27DAP	1.04637	0.56
41DAP/39DAP	1.09497	0.238
42DAP/41DAP	1.01193	0.999
43DAP/42DAP	1.07635	0.297
47DAP/43DAP	1.04008	0.749
52DAP/47DAP	1.15255	0.598
57DAP/52DAP	1.05367	0.783
57DAP/7DAP	0.96598	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.97545	0.55
17DAP/reference	1.01936	1
27DAP/reference	1.09338	0.551
39DAP/reference	1.06434	1
41DAP/reference	0.93266	0.298
42DAP/reference	0.95619	0.393
43DAP/reference	0.89215	0.159
47DAP/reference	0.848	0.079
52DAP/reference	1.11266	0.015
57DAP/reference	1.16049	0.035

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.93353	0.353
17DAP/reference	0.8404	0.102
27DAP/reference	0.92687	0.24
39DAP/reference	1.05511	0.705
41DAP/reference	1.13779	0.309
42DAP/reference	0.93446	0.321
43DAP/reference	0.88509	0.243
47DAP/reference	0.80236	0.029
52DAP/reference	0.89893	0.171
57DAP/reference	0.74227	0.023

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.94871	0.489
17DAP/reference	0.75792	0.011
27DAP/reference	0.92117	0.442
39DAP/reference	0.87705	0.179
41DAP/reference	0.9829	0.682
42DAP/reference	1.13845	0.3
43DAP/reference	0.92408	0.484
47DAP/reference	0.88557	0.224
52DAP/reference	1.2252	0.262
57DAP/reference	1.26597	0.03

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.87368	1
26DAP/20DAP	0.92896	0.512
34DAP/26DAP	1.12593	0.819
51DAP/34DAP	1.018	0.936
52DAP/51DAP	1.12089	0.288
53DAP/52DAP	0.9622	0.807
55DAP/53DAP	1.14243	0.434
57DAP/55DAP	0.92874	0.783
62DAP/57DAP	1.25064	0.868
68DAP/62DAP	1.00553	1
68DAP/14DAP	1.04562	0.958

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.88303	0.054

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.79656	0.256
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	N/A	N/A
Mature Eggplant/Ripe Tomato	0.64024	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	1.02847
12-2/M82	N/A	N/A
12-4/M82	1.07329	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	0.96046
4-1-1/M82	N/A	N/A
4-1/M82	N/A	N/A
4-3-2/M82	0.85951	0.412
4-3/M82	1.08454
5-3/M82	1.59885	0.436
6-2/M82	N/A	N/A
6-3/M82	0.99363
7-1/M82	N/A	N/A
7-2/M82	0.98625
9-3-2/M82	1.04804

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.34372	0.277
IL2-6/WTpooled	0.87694	0.473
IL7-5/WTpooled	0.96237	1
IL7-3/WTpooled	1.07701	0.362
IL12-4/WTpooled	1.02217	0.737
IL1-4/WTpooled	1.10837	1
WT/WTpooled	0.90608	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	1.01171	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.09152	0.921
DC3000/delta hrp 6h	N/A	N/A
DC3000/delta hrp 12h	N/A	N/A
DC3000/delta hrp 24h	0.68519	0.042

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.19994	0.229
DC3000 delta B/DC3000 delta AB	1.21648	0.23

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	N/A	N/A
Exp 36h	1.0053	1
Exp 60h	0.95254	0.855

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

hybridization	ratio	FDR (corrected p value)
self-self	0.97099	1
Var 0h	0.98011	1
Var 12h I row2-row1	0.94804	0.418
Var 12h NI row2-row1	1.07264	0.34
Var 36h I row2-row1	1.05021	1
Var 36h NI row2-row1	0.9764	0.791
Var 60h I row2-row1	0.85011	0.293
Var 60h NI row2-row1	1.00505	1
Time course 0hI-0hNI	0.97588	0.9
Time course 12hI-12hNI	1.02645	0.779
Time course 36hI-36hNI	1.23541	0.007
Time course 60hI-60hNI	1.80698	0.008

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)	0.91542	0.348
transgenic ySAMdc/azygous control (breaker)	1.42843	0.162
transgenic ySAMdc/azygous control (red)	1.09025	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.17238	0.063

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.23962	0.237

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.85103	1
Manapal/WT (break)	0.85965	0.333
Manapal/WT (red)	1.18616	0.133