Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.2.17.4

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.76751	0.232
27DAP/17DAP	0.62775	0.139
39DAP/27DAP	1.25056	0.903
41DAP/39DAP	1.19081	1
42DAP/41DAP	0.72978	0.397
43DAP/42DAP	1.22877	1
47DAP/43DAP	1.11439	0.809
52DAP/47DAP	1.49903	0.371
57DAP/52DAP	1.38999	0.859

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.15817	0.041
17DAP/reference	1.10484	0.083
27DAP/reference	1.28111	0.009
39DAP/reference	1.14957	0.061
41DAP/reference	1.05852	0.714
42DAP/reference	1.01232	1
43DAP/reference	1.15791	0.011
47DAP/reference	1.17414	0.031
52DAP/reference	1.02425	1
57DAP/reference	1.0488	0.682

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.30025	0.017
27DAP/17DAP	1.19529	0.122
39DAP/27DAP	0.89208	0.405
41DAP/39DAP	1.18644	1
42DAP/41DAP	1.11022	0.8
43DAP/42DAP	0.5509	0.022
47DAP/43DAP	0.99363	0.983
52DAP/47DAP	0.86626	0.226
57DAP/52DAP	0.94507	0.641
57DAP/7DAP	0.19925	0.186

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	2.07222	0.025
17DAP/reference	1.10425	0.477
27DAP/reference	1.25308	0.06
39DAP/reference	1.14676	0.149
41DAP/reference	1.18787	0.083
42DAP/reference	1.23873	0.059
43DAP/reference	0.91649	0.252
47DAP/reference	1.38766	0.121
52DAP/reference	0.89292	0.232
57DAP/reference	0.81756	0.015

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.23697	0.196
17DAP/reference	1.16627	0.127
27DAP/reference	1.21534	0.192
39DAP/reference	1.15233	0.2
41DAP/reference	1.28183	0.014
42DAP/reference	1.14109	0.033
43DAP/reference	0.92111	0.361
47DAP/reference	1.14781	0.101
52DAP/reference	1.08296	0.043
57DAP/reference	0.84054	0.107

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	2.20732	0.016
17DAP/reference	1.03721	0.887
27DAP/reference	1.00899	1
39DAP/reference	1.05838	0.451
41DAP/reference	0.99079	0.682
42DAP/reference	0.9821	0.671
43DAP/reference	0.95278	0.449
47DAP/reference	1.68714	0.008
52DAP/reference	1.36322	0.182
57DAP/reference	1.47384	0.009

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.05562	0.966
26DAP/20DAP	2.22406	0.098
34DAP/26DAP	0.74189	0.24
51DAP/34DAP	1.05197	0.993
52DAP/51DAP	0.98847	1
53DAP/52DAP	1.80249
55DAP/53DAP	1.15392	0.126
57DAP/55DAP	0.92433	0.652
62DAP/57DAP	0.9439	0.681
68DAP/62DAP	1.14364	0.85
68DAP/14DAP	1.08688	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	2.97209	0.014

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.65071	0.16
Mature Green Tomato/Ripe Tomato	1.78473	0.017
Immature Eggplant/Mature Eggplant	0.88048	0.407
Ripe Pepper/Ripe Tomato	0.63196	0.224
Mature Eggplant/Ripe Tomato	1.24441	0.373

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.93422	0.944
1-1-2/M82	1.01299	1
12-2/M82	1.08852	1
12-4/M82	0.80355	0.619
1-3/M82	1.87711	0.248
2-1-1/M82	0.81344	0.92
2-1/M82	0.88469
2-6/M82	1.14118	0.695
3-2/M82	0.93517
4-1-1/M82	N/A	N/A
4-1/M82	1.07826
4-3-2/M82	1.36156	0.508
4-3/M82	0.97729	1
5-3/M82	1.17017	0.572
6-2/M82	N/A	N/A
6-3/M82	0.91975	0.587
7-1/M82	0.94936	1
7-2/M82	1.23825	0.324
9-3-2/M82	1.03525	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.67991	0.243
IL2-6/WTpooled	0.60256	0.348
IL7-5/WTpooled	0.97992	1
IL7-3/WTpooled	0.78306	0.418
IL12-4/WTpooled	0.84476	0.581
IL1-4/WTpooled	0.60117	0.415
WT/WTpooled	1.07917	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	1.32984	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.95435	1
DC3000/delta hrp 6h	1.06404	1
DC3000/delta hrp 12h	1.04255	1
DC3000/delta hrp 24h	1.99488	0.221

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	1.25975	0.212

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.05972	1
Exp 36h	1.84827	0.693
Exp 60h	1.02336	1

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

hybridization	ratio	FDR (corrected p value)
self-self	1.01689	1
Var 0h	1.21936	0.782
Var 12h I row2-row1	1.2373	0.208
Var 12h NI row2-row1	1.28335	0.34
Var 36h I row2-row1	1.01707	1
Var 36h NI row2-row1	1.1654	1
Var 60h I row2-row1	0.66791	0.374
Var 60h NI row2-row1	0.73773	0.359
Time course 0hI-0hNI	1.0273	1
Time course 12hI-12hNI	1.68895	0.004
Time course 36hI-36hNI	2.13619	0.004
Time course 60hI-60hNI	4.19801	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)	1.25828	0.272
transgenic ySAMdc/azygous control (breaker)	0.66868	0.142
transgenic ySAMdc/azygous control (red)	0.81216	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.39801	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.57067	0.172
Manapal/WT (break)	0.83636	0.333
Manapal/WT (red)	0.60618	0.181