Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.1.7.21

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.20485	0.545
27DAP/17DAP	1.0182	0.926
39DAP/27DAP	0.97921	0.749
41DAP/39DAP	0.99852	0.919
42DAP/41DAP	1.03747	0.978
43DAP/42DAP	1.00105	0.937
47DAP/43DAP	1.1342	0.647
52DAP/47DAP	0.98564	0.908
57DAP/52DAP	0.99244	0.983

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.40521	0.033
17DAP/reference	1.10889	0.239
27DAP/reference	0.85739	0.075
39DAP/reference	0.97685	0.704
41DAP/reference	1.02488	1
42DAP/reference	1.29519	0.001
43DAP/reference	1.22262	0.011
47DAP/reference	1.12931	0.114
52DAP/reference	0.92789	0.215
57DAP/reference	1.12056	0.211

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.10887	0.414
27DAP/17DAP	1.22023	0.295
39DAP/27DAP	1.06748	0.623
41DAP/39DAP	1.07032	0.69
42DAP/41DAP	0.97557	0.732
43DAP/42DAP	1.04539	0.513
47DAP/43DAP	1.01505	0.973
52DAP/47DAP	1.03958	0.945
57DAP/52DAP	0.961	0.564
57DAP/7DAP	1.04441	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.56495	0.024
17DAP/reference	1.25436	0.077
27DAP/reference	1.30561	0.049
39DAP/reference	1.27756	0.056
41DAP/reference	1.20306	0.043
42DAP/reference	1.36573	0.021
43DAP/reference	1.31723	0.053
47DAP/reference	1.33094	0.057
52DAP/reference	1.48986	0.011
57DAP/reference	1.35669	0.004

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.18136	0.39
17DAP/reference	1.3386	0.03
27DAP/reference	1.36239	0.04
39DAP/reference	1.23837	0.039
41DAP/reference	1.04635	0.737
42DAP/reference	1.14073	0.302
43DAP/reference	1.06781	0.801
47DAP/reference	1.34507	0.046
52DAP/reference	0.81918	0.04
57DAP/reference	0.99256	0.72

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.03381	0.723
17DAP/reference	0.88572	0.172
27DAP/reference	1.24464	0.031
39DAP/reference	1.25935	0.023
41DAP/reference	1.16543	0.021
42DAP/reference	1.06792	0.6
43DAP/reference	1.3205	0.062
47DAP/reference	0.9316	0.231
52DAP/reference	1.24417	0.436
57DAP/reference	1.18477	0.291

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.88209	1
26DAP/20DAP	0.91555	1
34DAP/26DAP	0.97085	0.936
51DAP/34DAP	1.29549	0.483
52DAP/51DAP	0.84312	0.07
53DAP/52DAP	1.05811	0.882
55DAP/53DAP	0.93198	0.336
57DAP/55DAP	1.04561	1
62DAP/57DAP	1.33472	0.723
68DAP/62DAP	0.94266
68DAP/14DAP	0.51997

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.16021	0.391

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.2283	0.075
Mature Green Tomato/Ripe Tomato	1.07144	0.752
Immature Eggplant/Mature Eggplant	1.05116	0.417
Ripe Pepper/Ripe Tomato	1.26383	1
Mature Eggplant/Ripe Tomato	1.15177	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.84792	0.944
1-1-2/M82	1.06923	1
12-2/M82	0.60088	0.727
12-4/M82	0.86137	0.619
1-3/M82	2.16593
2-1-1/M82	1.04228	1
2-1/M82	0.65396
2-6/M82	0.77431	1
3-2/M82	1.31722	0.84
4-1-1/M82	0.67871	1
4-1/M82	0.94802	1
4-3-2/M82	1.06731	1
4-3/M82	1.12826	1
5-3/M82	1.09311	0.572
6-2/M82	0.93722
6-3/M82	0.92222	1
7-1/M82	1.14849	0.598
7-2/M82	1.23133	0.302
9-3-2/M82	0.90031	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	N/A	N/A
IL1-4/WTpooled	N/A	N/A
WT/WTpooled	N/A	N/A

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	1.16441	0.699

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.07828	0.894
DC3000/delta hrp 6h	0.85289	0.95
DC3000/delta hrp 12h	0.96237	1
DC3000/delta hrp 24h	1.13701	0.347

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.11116	0.333
DC3000 delta B/DC3000 delta AB	1.16522	0.394

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.9139	1
Exp 36h	1.32502	0.693
Exp 60h	1.16812	0.563

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

hybridization	ratio	FDR (corrected p value)
self-self	1.03365	1
Var 0h	0.53192	0.421
Var 12h I row2-row1	0.8762	0.338
Var 12h NI row2-row1	0.84258	1
Var 36h I row2-row1	1.13195	0.742
Var 36h NI row2-row1	0.9597	0.706
Var 60h I row2-row1	0.8851	0.285
Var 60h NI row2-row1	0.76666	0.306
Time course 0hI-0hNI	1.04581	0.799
Time course 12hI-12hNI	1.02008	0.88
Time course 36hI-36hNI	1.46713	0.005
Time course 60hI-60hNI	2.63373	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)	0.93472	0.485
transgenic ySAMdc/azygous control (breaker)	1.72733	0.178
transgenic ySAMdc/azygous control (red)	1.30179	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.21816	0.092

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.81367	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.92945	1
Manapal/WT (break)	1.0244	1
Manapal/WT (red)	1.09924	0.137