Tomato Functional Genomics Database (TFGD)

Expression of 1-1-5.2.4.12

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.97502	0.801
27DAP/17DAP	1.09332	0.92
39DAP/27DAP	1.29355	0.8
41DAP/39DAP	1.01373	0.988
42DAP/41DAP	1.05151	0.992
43DAP/42DAP	1.19529	0.88
47DAP/43DAP	0.8125	0.42
52DAP/47DAP	1.1272	0.98
57DAP/52DAP	1.15982	0.946

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.92487	0.2
17DAP/reference	0.85887	0.041
27DAP/reference	0.98026	0.668
39DAP/reference	0.86017	0.074
41DAP/reference	0.83981	0.011
42DAP/reference	1.02789	1
43DAP/reference	1.02879	0.758
47DAP/reference	1.1144	0.136
52DAP/reference	1.10319	0.242
57DAP/reference	1.11697	0.101

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.14633	0.196
27DAP/17DAP	1.30321	0.117
39DAP/27DAP	0.84771	0.176
41DAP/39DAP	1.08484	0.801
42DAP/41DAP	1.0077	0.899
43DAP/42DAP	0.79921	0.093
47DAP/43DAP	1.24804	0.066
52DAP/47DAP	0.94634	0.777
57DAP/52DAP	1.1264	0.427
57DAP/7DAP	0.6687	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.4743	0.033
17DAP/reference	1.25586	0.014
27DAP/reference	1.37965	0.035
39DAP/reference	1.28023	0.009
41DAP/reference	1.48003	0.02
42DAP/reference	1.42797	0.007
43DAP/reference	1.37164	0.023
47DAP/reference	1.29612	0.161
52DAP/reference	1.3343	0.046
57DAP/reference	1.21381	0.022

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.1344	0.767
17DAP/reference	0.85973	0.134
27DAP/reference	1.00417	1
39DAP/reference	1.14167	0.128
41DAP/reference	0.89443	0.403
42DAP/reference	1.11859	0.254
43DAP/reference	0.82363	0.072
47DAP/reference	0.93036	0.302
52DAP/reference	1.30367	0.444
57DAP/reference	0.94019	0.488

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.37447	0.032
17DAP/reference	1.05802	0.531
27DAP/reference	1.10318	0.26
39DAP/reference	1.09173	0.307
41DAP/reference	1.11949	0.397
42DAP/reference	1.08473	0.576
43DAP/reference	1.07094	0.572
47DAP/reference	0.95086	0.383
52DAP/reference	1.3561	0.072
57DAP/reference	1.12731	0.592

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.12349	0.966
26DAP/20DAP	1.1836	0.322
34DAP/26DAP	1.64192	0.154
51DAP/34DAP	1.10012	0.692
52DAP/51DAP	1.61673	0.556
53DAP/52DAP	0.77396	0.157
55DAP/53DAP	0.97792	0.784
57DAP/55DAP	0.87544	0.601
62DAP/57DAP	1.463	0.8
68DAP/62DAP	1.22617	0.778
68DAP/14DAP	3.08172	0.311

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	2.12386	0.229

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.66587	0.174
Mature Green Tomato/Ripe Tomato	1.29231	0.399
Immature Eggplant/Mature Eggplant	1.16499	0.19
Ripe Pepper/Ripe Tomato	0.94218	1
Mature Eggplant/Ripe Tomato	0.88683	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.02208	1
1-1-2/M82	1.03311	1
12-2/M82	0.79034
12-4/M82	0.7687	0.33
1-3/M82	1.7605	0.277
2-1-1/M82	1.11566	1
2-1/M82	0.93076	0.74
2-6/M82	0.75487	1
3-2/M82	1.10587	0.967
4-1-1/M82	0.95019	1
4-1/M82	N/A	N/A
4-3-2/M82	1.09887
4-3/M82	1.13945	1
5-3/M82	1.25079	0.496
6-2/M82	1.36931	0.188
6-3/M82	1.0189	1
7-1/M82	1.15935	1
7-2/M82	1.20375	0.302
9-3-2/M82	1.21692	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	1.10274	1
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.86904	0.418
IL12-4/WTpooled	0.90782	0.484
IL1-4/WTpooled	1.39503
WT/WTpooled	0.98347	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	1.22711	0.309

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.27853	0.823
DC3000/delta hrp 6h	0.93781	0.95
DC3000/delta hrp 12h	0.94969	1
DC3000/delta hrp 24h	1.54798	0.03

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.21627	0.208
DC3000 delta B/DC3000 delta AB	0.81433	0.11

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.93822	1
Exp 36h	1.28809	0.409
Exp 60h	1.28695	0.563

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

hybridization	ratio	FDR (corrected p value)
self-self	N/A	N/A
Var 0h	N/A	N/A
Var 12h I row2-row1	N/A	N/A
Var 12h NI row2-row1	N/A	N/A
Var 36h I row2-row1	N/A	N/A
Var 36h NI row2-row1	N/A	N/A
Var 60h I row2-row1	N/A	N/A
Var 60h NI row2-row1	N/A	N/A
Time course 0hI-0hNI	N/A	N/A
Time course 12hI-12hNI	N/A	N/A
Time course 36hI-36hNI	N/A	N/A
Time course 60hI-60hNI	N/A	N/A

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)	0.98677	0.567
transgenic ySAMdc/azygous control (breaker)	1.01338	1
transgenic ySAMdc/azygous control (red)	1.06112	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.03806	0.135

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.47393	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.67486	0.172
Manapal/WT (break)	0.79296	0.255
Manapal/WT (red)	0.88819	0.424