Tomato Functional Genomics Database (TFGD)

Expression of 1-1-5.3.7.12

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.85405	0.419
27DAP/17DAP	0.99801	0.996
39DAP/27DAP	1.41989	0.265
41DAP/39DAP	0.72821	0.15
42DAP/41DAP	1.18451	0.863
43DAP/42DAP	1.07281	1
47DAP/43DAP	1.19955	0.527
52DAP/47DAP	1.21881	0.63
57DAP/52DAP	1.08588	0.977

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.96595	0.476
17DAP/reference	0.79838	0.007
27DAP/reference	0.81765	0.03
39DAP/reference	0.85493	0.132
41DAP/reference	0.72322	0.008
42DAP/reference	0.91794	0.157
43DAP/reference	0.85767	0.061
47DAP/reference	1.014	0.636
52DAP/reference	1.36077	0.053
57DAP/reference	1.29741	0.026

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.95281	0.629
27DAP/17DAP	1.12474	0.909
39DAP/27DAP	0.95119	0.737
41DAP/39DAP	1.12548	0.807
42DAP/41DAP	1.08554	0.615
43DAP/42DAP	1.10434	0.699
47DAP/43DAP	0.96866	0.886
52DAP/47DAP	0.85926	0.466
57DAP/52DAP	0.97918	0.784
57DAP/7DAP	0.95778	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.24865	0.177
17DAP/reference	1.50497	0.02
27DAP/reference	1.54812	0.026
39DAP/reference	1.25792	0.056
41DAP/reference	1.43464	0.018
42DAP/reference	1.41849	0.059
43DAP/reference	1.54011	0.043
47DAP/reference	1.17952	0.44
52DAP/reference	1.4289	0.007
57DAP/reference	1.32236	0.214

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.74876	0.012
17DAP/reference	0.80053	0.016
27DAP/reference	1.05944	0.834
39DAP/reference	1.22656	0.324
41DAP/reference	1.18902	0.309
42DAP/reference	0.93158	0.392
43DAP/reference	0.76082	0.043
47DAP/reference	0.7944	0.019
52DAP/reference	1.14313	0.065
57DAP/reference	0.78495	0.03

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.98014	0.455
17DAP/reference	1.33784	0.462
27DAP/reference	1.44063	0.024
39DAP/reference	1.39301	0.02
41DAP/reference	1.38413	0.025
42DAP/reference	1.64789	0.01
43DAP/reference	1.84636	0.008
47DAP/reference	0.78497	0.224
52DAP/reference	1.38242	0.278
57DAP/reference	1.85554	0.016

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.22061	0.966
26DAP/20DAP	1.00345	1
34DAP/26DAP	0.90375	0.61
51DAP/34DAP	0.92968	0.624
52DAP/51DAP	0.69022	1
53DAP/52DAP	1.26777	0.643
55DAP/53DAP	0.89651	0.085
57DAP/55DAP	0.80425	0.256
62DAP/57DAP	1.59097	0.098
68DAP/62DAP	1.47474	0.214
68DAP/14DAP	2.03435	0.051

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.00666	0.696

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.91859	0.569
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	1.71034	0.239
Mature Eggplant/Ripe Tomato	1.54099	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.84178	0.883
1-1-2/M82	1.15458	1
12-2/M82	0.75548	0.678
12-4/M82	1.13937	1
1-3/M82	1.69156	0.248
2-1-1/M82	0.83953
2-1/M82	N/A	N/A
2-6/M82	1.15157
3-2/M82	N/A	N/A
4-1-1/M82	1.12155	1
4-1/M82	0.70518
4-3-2/M82	1.28586
4-3/M82	1.24326	1
5-3/M82	1.25047	0.496
6-2/M82	1.37937
6-3/M82	0.78862	1
7-1/M82	N/A	N/A
7-2/M82	1.20152	1
9-3-2/M82	1.57777

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	2.71491	0.277
IL2-6/WTpooled	0.82396	0.337
IL7-5/WTpooled	1.46932
IL7-3/WTpooled	1.51817	1
IL12-4/WTpooled	1.36827	0.624
IL1-4/WTpooled	2.53182	1
WT/WTpooled	0.86973	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	1.21539	0.699

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.98469	1
DC3000/delta hrp 6h	1.3526	0.777
DC3000/delta hrp 12h	1.00458	1
DC3000/delta hrp 24h	0.66863	0.04

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.86605	0.92
DC3000 delta B/DC3000 delta AB	0.93871	0.589

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	0.98268	1
Var 0h	0.90688	0.255
Var 12h I row2-row1	0.97038	0.77
Var 12h NI row2-row1	1.00197	1
Var 36h I row2-row1	1.12238	0.908
Var 36h NI row2-row1	1.47874	1
Var 60h I row2-row1	0.97993	1
Var 60h NI row2-row1	1.05593	0.904
Time course 0hI-0hNI	1.03001	0.852
Time course 12hI-12hNI	0.96444	0.79
Time course 36hI-36hNI	1.02061	0.975
Time course 60hI-60hNI	0.84674	0.015

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)	0.93361	0.614
transgenic ySAMdc/azygous control (breaker)	0.39779	0.131
transgenic ySAMdc/azygous control (red)	1.02689	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.96533	0.323

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.16106	0.277

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.49308	0.088
Manapal/WT (break)	0.81605	1
Manapal/WT (red)	0.99759	0.863