Tomato Functional Genomics Database (TFGD)

Expression of 1-1-4.2.10.12

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.08385	0.947
27DAP/17DAP	0.85067	0.609
39DAP/27DAP	1.81322	0.163
41DAP/39DAP	1.24847	0.772
42DAP/41DAP	1.11409	0.916
43DAP/42DAP	1.06854	1
47DAP/43DAP	0.66081	0.102
52DAP/47DAP	0.96232	0.875
57DAP/52DAP	1.46906	0.648

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.36851	0.016
17DAP/reference	1.02377	0.696
27DAP/reference	1.03847	0.759
39DAP/reference	1.02121	0.76
41DAP/reference	1.04152	0.552
42DAP/reference	1.23823	0.006
43DAP/reference	1.20541	0.083
47DAP/reference	1.19624	0.078
52DAP/reference	1.16627	0.011
57DAP/reference	0.98396	0.58

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.86116	0.402
27DAP/17DAP	1.18197	0.645
39DAP/27DAP	1.71617	0.174
41DAP/39DAP	3.24964	0.005
42DAP/41DAP	0.67054	0.016
43DAP/42DAP	0.66909	0.026
47DAP/43DAP	1.19123	0.293
52DAP/47DAP	0.87849	0.572
57DAP/52DAP	0.60573	0.17
57DAP/7DAP	0.82866	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.51151	0.03
17DAP/reference	1.35773	0.054
27DAP/reference	1.09746	0.301
39DAP/reference	1.28173	0.021
41DAP/reference	1.16823	0.241
42DAP/reference	1.30765	0.024
43DAP/reference	1.54605	0.006
47DAP/reference	1.47391	0.033
52DAP/reference	1.23796	0.025
57DAP/reference	1.26798	0.005

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.34028	0.049
17DAP/reference	1.3815	0.018
27DAP/reference	1.29175	0.049
39DAP/reference	1.10994	0.449
41DAP/reference	1.00405	0.493
42DAP/reference	1.04068	1
43DAP/reference	0.98761	0.67
47DAP/reference	1.08985	0.603
52DAP/reference	1.06831	0.417
57DAP/reference	0.91622	0.259

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.56012	0.02
17DAP/reference	1.11317	0.365
27DAP/reference	1.14207	0.164
39DAP/reference	1.15012	0.03
41DAP/reference	1.08583	0.621
42DAP/reference	1.3229	0.027
43DAP/reference	1.74213	0.01
47DAP/reference	1.2737	0.063
52DAP/reference	1.14601	0.278
57DAP/reference	1.31653	0.187

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.71018	1
26DAP/20DAP	1.29789	0.46
34DAP/26DAP	1.0974	1
51DAP/34DAP	1.0057	0.856
52DAP/51DAP	0.76359	1
53DAP/52DAP	1.20753	0.882
55DAP/53DAP	1.05576	0.834
57DAP/55DAP	1.2427	0.626
62DAP/57DAP	0.58021	0.004
68DAP/62DAP	0.7406	0.505
68DAP/14DAP	0.97202	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.67323	0.113

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.8101	0.265
Mature Green Tomato/Ripe Tomato	1.2903	0.363
Immature Eggplant/Mature Eggplant	0.74892	0.069
Ripe Pepper/Ripe Tomato	2.18782	0.256
Mature Eggplant/Ripe Tomato	1.38977	0.26

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	N/A	N/A
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	N/A	N/A
4-3/M82	N/A	N/A
5-3/M82	N/A	N/A
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	1.02311
IL2-6/WTpooled	0.96563
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	0.93842	1
IL1-4/WTpooled	1.41553	1
WT/WTpooled	1.10958	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	1.63667	0.699

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.00571	1
DC3000/delta hrp 6h	1.16357	1
DC3000/delta hrp 12h	1.19907	1
DC3000/delta hrp 24h	1.06441	0.62

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.76046	0.042
DC3000 delta B/DC3000 delta AB	3.52974	0.023

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.02156	1
Exp 36h	0.98901	0.943
Exp 60h	0.95093	0.855

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

hybridization	ratio	FDR (corrected p value)
self-self	0.97163	1
Var 0h	0.52349	0.339
Var 12h I row2-row1	0.83427	0.627
Var 12h NI row2-row1	2.34412	0.235
Var 36h I row2-row1	1.39116	1
Var 36h NI row2-row1	0.47503	0.478
Var 60h I row2-row1	0.85254	0.582
Var 60h NI row2-row1	0.54772	0.306
Time course 0hI-0hNI	1.53503	0.603
Time course 12hI-12hNI	1.42238	0.65
Time course 36hI-36hNI	6.44036	0.004
Time course 60hI-60hNI	30.3466	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)	0.87905	0.246
transgenic ySAMdc/azygous control (breaker)	0.61633	0.134
transgenic ySAMdc/azygous control (red)	0.98601	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.09833	0.047

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.72897	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.08955	1
Manapal/WT (break)	0.72928	0.299
Manapal/WT (red)	0.96694	0.863