Tomato Functional Genomics Database (TFGD)

Expression of 1-1-5.3.20.11

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.01566	0.927
27DAP/17DAP	1.29745	0.758
39DAP/27DAP	0.93986	0.631
41DAP/39DAP	1.25943	0.339
42DAP/41DAP	0.95436	1
43DAP/42DAP	1.0724	1
47DAP/43DAP	1.16784	0.497
52DAP/47DAP	0.79257	0.498
57DAP/52DAP	1.02246	1

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.97995	0.578
17DAP/reference	0.99265	0.858
27DAP/reference	1.02527	0.847
39DAP/reference	1.00048	1
41DAP/reference	0.95011	0.542
42DAP/reference	0.95144	0.075
43DAP/reference	1.0245	0.838
47DAP/reference	0.94867	0.322
52DAP/reference	0.94658	0.393
57DAP/reference	0.9842	0.58

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.66315	0.131
27DAP/17DAP	1.20479	0.527
39DAP/27DAP	1.34175	0.646
41DAP/39DAP	1.70522	0.027
42DAP/41DAP	0.73975	0.009
43DAP/42DAP	0.95416	0.684
47DAP/43DAP	1.24045	0.051
52DAP/47DAP	0.8986	0.645
57DAP/52DAP	1.27718	0.274
57DAP/7DAP	1.01945	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.52057	0.036
17DAP/reference	1.70489	0.006
27DAP/reference	1.34173	0.015
39DAP/reference	1.67586	0.007
41DAP/reference	1.96737	0.014
42DAP/reference	1.81447	0.007
43DAP/reference	2.2648	0.007
47DAP/reference	1.64484	0.02
52DAP/reference	1.66782	0.017
57DAP/reference	1.98974	0.004

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.88757	0.06
17DAP/reference	0.82564	0.034
27DAP/reference	0.98813	0.619
39DAP/reference	0.85924	0.072
41DAP/reference	0.9516	0.115
42DAP/reference	0.87396	0.067
43DAP/reference	0.8062	0.102
47DAP/reference	0.91375	0.025
52DAP/reference	0.77441	0.004
57DAP/reference	0.86835	0.135

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.15996	0.07
17DAP/reference	1.0119	0.9
27DAP/reference	1.38057	0.028
39DAP/reference	1.27441	0.018
41DAP/reference	1.24846	0.115
42DAP/reference	1.27503	0.021
43DAP/reference	1.22483	0.194
47DAP/reference	1.21553	0.048
52DAP/reference	1.71579	0.036
57DAP/reference	1.21929	0.223

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.90225	0.997
26DAP/20DAP	1.18758	0.916
34DAP/26DAP	1.17359	0.819
51DAP/34DAP	0.74392	0.117
52DAP/51DAP	1.32844	0.099
53DAP/52DAP	0.85851	0.202
55DAP/53DAP	1.54268	0.061
57DAP/55DAP	0.86162	0.391
62DAP/57DAP	1.37815	0.185
68DAP/62DAP	1.36207	0.162
68DAP/14DAP	0.96149	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.57526	0.02

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.48608	0.087
Mature Green Tomato/Ripe Tomato	0.65377	0.014
Immature Eggplant/Mature Eggplant	0.58169	0.063
Ripe Pepper/Ripe Tomato	1.29167	1
Mature Eggplant/Ripe Tomato	0.74507	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	0.92961	1
12-2/M82	1.08159
12-4/M82	0.91971	1
1-3/M82	N/A	N/A
2-1-1/M82	N/A	N/A
2-1/M82	1.01242
2-6/M82	1.17686	0.594
3-2/M82	0.95575	1
4-1-1/M82	0.903
4-1/M82	0.9398	1
4-3-2/M82	1.08375
4-3/M82	1.31774	1
5-3/M82	1.12775	0.572
6-2/M82	1.96805	1
6-3/M82	0.81568
7-1/M82	N/A	N/A
7-2/M82	1.34474
9-3-2/M82	0.93974	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	1.03519	1
IL12-4/WTpooled	1.46538	0.48
IL1-4/WTpooled	1.0167	1
WT/WTpooled	1.04631	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	1.19635	0.309

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.1025	0.921
DC3000/delta hrp 6h	0.87468	0.95
DC3000/delta hrp 12h	1.02542	1
DC3000/delta hrp 24h	2.14253	0.044

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.94468	0.145
DC3000 delta B/DC3000 delta AB	1.31877	0.201

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.33492	0.228
Exp 36h	1.81926	0.326
Exp 60h	1.90077	0.221

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

hybridization	ratio	FDR (corrected p value)
self-self	0.95012	1
Var 0h	N/A	N/A
Var 12h I row2-row1	1.30457	0.195
Var 12h NI row2-row1	1.35364	0.649
Var 36h I row2-row1	1.11462	0.908
Var 36h NI row2-row1	1.12596	1
Var 60h I row2-row1	0.75855	0.293
Var 60h NI row2-row1	1.01801	1
Time course 0hI-0hNI	1.14591	0.574
Time course 12hI-12hNI	2.10354	0.006
Time course 36hI-36hNI	2.60592	0.005
Time course 60hI-60hNI	3.67981	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)	1.079	0.294
transgenic ySAMdc/azygous control (breaker)	0.74482	0.139
transgenic ySAMdc/azygous control (red)	1.12989	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.09072	0.17

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.18279	0.239

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.83738	0.172
Manapal/WT (break)	0.85586	0.333
Manapal/WT (red)	0.79262	0.242