Tomato Functional Genomics Database (TFGD)

Expression of 1-1-6.2.19.14

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.15462	0.561
27DAP/17DAP	1.18777	0.825
39DAP/27DAP	0.76028	0.462
41DAP/39DAP	1.5824	0.264
42DAP/41DAP	1.02389	1
43DAP/42DAP	1.01011	1
47DAP/43DAP	1.12498	0.647
52DAP/47DAP	1.13824	0.767
57DAP/52DAP	0.85001	0.74

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.3139	0.057
17DAP/reference	1.30435	0.022
27DAP/reference	1.29881	0.146
39DAP/reference	1.21618	0.14
41DAP/reference	1.62923	0.012
42DAP/reference	1.39791	0.002
43DAP/reference	1.21504	0.142
47DAP/reference	1.29827	0.006
52DAP/reference	1.28912	0.031
57DAP/reference	1.04608	0.767

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.94149	0.428
27DAP/17DAP	0.9579	0.782
39DAP/27DAP	0.99812	1
41DAP/39DAP	1.15203	0.69
42DAP/41DAP	0.91398	0.436
43DAP/42DAP	1.02603	0.513
47DAP/43DAP	0.98981	0.947
52DAP/47DAP	1.0109	0.991
57DAP/52DAP	1.04436	0.722
57DAP/7DAP	1.06781	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.84735	0.082
17DAP/reference	0.81282	0.011
27DAP/reference	0.82502	0.013
39DAP/reference	0.81839	0.014
41DAP/reference	0.82586	0.111
42DAP/reference	0.82294	0.032
43DAP/reference	0.75223	0.016
47DAP/reference	1.0416	1
52DAP/reference	0.66329	0.024
57DAP/reference	0.79853	0.007

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.33658	0.151
17DAP/reference	2.13113	0.017
27DAP/reference	1.35987	0.037
39DAP/reference	1.41657	0.013
41DAP/reference	1.5982	0.005
42DAP/reference	1.55431	0.024
43DAP/reference	2.60269	0.065
47DAP/reference	1.26162	0.01
52DAP/reference	1.75826	0.008
57DAP/reference	1.1884	0.581

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.02703	0.699
17DAP/reference	1.21302	0.405
27DAP/reference	0.85706	0.113
39DAP/reference	1.06219	0.643
41DAP/reference	0.80871	0.037
42DAP/reference	0.94632	0.445
43DAP/reference	0.94029	0.449
47DAP/reference	1.65044	0.014
52DAP/reference	0.72975	0.109
57DAP/reference	0.95968	0.475

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.56341	0.817
26DAP/20DAP	0.92534	0.317
34DAP/26DAP	1.08286	0.819
51DAP/34DAP	0.91441	0.369
52DAP/51DAP	1.031	0.776
53DAP/52DAP	0.95111	0.767
55DAP/53DAP	1.01325	0.964
57DAP/55DAP	1.03675	0.947
62DAP/57DAP	1.04558	1
68DAP/62DAP	1.29193	0.984
68DAP/14DAP	0.90207	0.375

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.81029	0.036

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.85101	0.347
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	N/A	N/A
Mature Eggplant/Ripe Tomato	0.61764

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.94557	0.944
1-1-2/M82	0.85899	0.958
12-2/M82	1.22347	1
12-4/M82	0.98332	1
1-3/M82	0.83645	0.378
2-1-1/M82	1.12844	0.764
2-1/M82	N/A	N/A
2-6/M82	1.14298	0.594
3-2/M82	0.89417
4-1-1/M82	0.99162	1
4-1/M82	1.28781
4-3-2/M82	0.77738	0.487
4-3/M82	0.78105	0.72
5-3/M82	0.85554	0.642
6-2/M82	0.89847	1
6-3/M82	1.04385	1
7-1/M82	1.12574	0.992
7-2/M82	0.97673	1
9-3-2/M82	0.75402

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	0.90936	0.473
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.71104	0.418
IL12-4/WTpooled	0.81833	0.71
IL1-4/WTpooled	1.15038
WT/WTpooled	1.03165	0.957

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	0.97863	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.01544	1
DC3000/delta hrp 6h	2.19735
DC3000/delta hrp 12h	1.15498	1
DC3000/delta hrp 24h	0.98542	0.978

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.60806	0.024
DC3000 delta B/DC3000 delta AB	0.60864	0.02

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	N/A	N/A
Exp 36h	N/A	N/A
Exp 60h	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
self-self	1.00261	1
Var 0h	1.63786	0.936
Var 12h I row2-row1	0.77159	0.353
Var 12h NI row2-row1	0.93569	0.627
Var 36h I row2-row1	0.92962	0.575
Var 36h NI row2-row1	1.18723	0.482
Var 60h I row2-row1	1.20848	0.562
Var 60h NI row2-row1	1.05889	0.904
Time course 0hI-0hNI	1.0231	0.867
Time course 12hI-12hNI	0.97896	0.87
Time course 36hI-36hNI	0.8721	0.067
Time course 60hI-60hNI	0.27922	0.005

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)	0.84317	0.391
transgenic ySAMdc/azygous control (breaker)	0.99011	1
transgenic ySAMdc/azygous control (red)	0.90918	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.85464	0.072

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.37954	0.223

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.41838	0.14
Manapal/WT (break)	1.25177	0.381
Manapal/WT (red)	2.33465	0.137