Tomato Functional Genomics Database (TFGD)

Expression of 1-1-4.4.12.21

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.87285	0.272
27DAP/17DAP	1.02998	0.956
39DAP/27DAP	1.36406	0.184
41DAP/39DAP	1.96857	0.286
42DAP/41DAP	5.66697	0.016
43DAP/42DAP	2.66921	0.491
47DAP/43DAP	1.47213	0.349
52DAP/47DAP	0.43208	0.044
57DAP/52DAP	1.56517	0.55

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	2.12138	0.007
17DAP/reference	1.56	0.053
27DAP/reference	1.86069	0.014
39DAP/reference	1.0205	0.901
41DAP/reference	0.89816	0.341
42DAP/reference	1.55969	0.001
43DAP/reference	0.94135	0.464
47DAP/reference	0.99906	0.568
52DAP/reference	0.74917	0.079
57DAP/reference	0.98319	0.58

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.98858	0.782
27DAP/17DAP	1.07817	0.751
39DAP/27DAP	1.05546	0.623
41DAP/39DAP	0.97867	0.973
42DAP/41DAP	0.98417	0.784
43DAP/42DAP	1.35651	0.134
47DAP/43DAP	1.07096	0.848
52DAP/47DAP	1.52698	0.147
57DAP/52DAP	1.11479	0.703
57DAP/7DAP	1.70543	0.249

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.99382	0.025
17DAP/reference	1.26871	0.064
27DAP/reference	0.94711	0.2
39DAP/reference	0.84204	0.031
41DAP/reference	0.74443	0.023
42DAP/reference	0.8999	0.13
43DAP/reference	0.94869	0.22
47DAP/reference	0.70487	0.03
52DAP/reference	0.7873	0.012
57DAP/reference	0.80459	0.086

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.60229	0.054
17DAP/reference	1.91401	0.007
27DAP/reference	1.49131	0.028
39DAP/reference	0.82675	0.136
41DAP/reference	1.07461	0.629
42DAP/reference	1.24006	0.118
43DAP/reference	0.6939	0.004
47DAP/reference	0.83598	0.022
52DAP/reference	0.67338	0.004
57DAP/reference	0.71445	0.014

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	2.29585	0.015
17DAP/reference	1.6004	0.057
27DAP/reference	1.62346	0.02
39DAP/reference	1.13857	0.059
41DAP/reference	1.00236	1
42DAP/reference	1.09444	0.716
43DAP/reference	1.18628	0.209
47DAP/reference	0.92195	0.325
52DAP/reference	0.86189	0.25
57DAP/reference	1.16707	0.549

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.98974	1
26DAP/20DAP	0.99109	1
34DAP/26DAP	1.07414	1
51DAP/34DAP	1.20904	0.143
52DAP/51DAP	0.97836	1
53DAP/52DAP	1.1158	0.712
55DAP/53DAP	0.98371	0.796
57DAP/55DAP	0.91662	0.59
62DAP/57DAP	1.363	0.098
68DAP/62DAP	0.97554	0.81
68DAP/14DAP	0.62027	0.086

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	4.01819	0.017

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.40085	0.058
Mature Green Tomato/Ripe Tomato	0.0431	0.014
Immature Eggplant/Mature Eggplant	0.28853	0.057
Ripe Pepper/Ripe Tomato	10.1187	0.236
Mature Eggplant/Ripe Tomato	27.7729	0.268

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	N/A	N/A
12-2/M82	N/A	N/A
12-4/M82	3.17294	1
1-3/M82	N/A	N/A
2-1-1/M82	N/A	N/A
2-1/M82	N/A	N/A
2-6/M82	N/A	N/A
3-2/M82	N/A	N/A
4-1-1/M82	N/A	N/A
4-1/M82	N/A	N/A
4-3-2/M82	3.19727
4-3/M82	N/A	N/A
5-3/M82	N/A	N/A
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	N/A	N/A
9-3-2/M82	1.43608

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.13612
IL2-6/WTpooled	0.94875	1
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.75789
IL12-4/WTpooled	0.73865	0.543
IL1-4/WTpooled	1.08578
WT/WTpooled	1.02282	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	0.79621	0.75

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.04734	0.921
DC3000/delta hrp 6h	1.05123	1
DC3000/delta hrp 12h	1.05221	1
DC3000/delta hrp 24h	0.39148	0.034

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.06699
DC3000 delta B/DC3000 delta AB	1.14096	0.311

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.88117	0.328
Exp 36h	0.78514	0.504
Exp 60h	0.66394	0.258

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

hybridization	ratio	FDR (corrected p value)
self-self	1.02532	1
Var 0h	0.98502	1
Var 12h I row2-row1	0.77817	0.418
Var 12h NI row2-row1	1.17653	0.649
Var 36h I row2-row1	1.0948	1
Var 36h NI row2-row1	0.63266	0.584
Var 60h I row2-row1	0.79103	0.582
Var 60h NI row2-row1	0.91268	0.866
Time course 0hI-0hNI	1.03169	0.63
Time course 12hI-12hNI	1.00906	1
Time course 36hI-36hNI	1.28515	0.01
Time course 60hI-60hNI	2.29511	0.022

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)	0.98211	0.722
transgenic ySAMdc/azygous control (breaker)	0.82204	0.49
transgenic ySAMdc/azygous control (red)	3.35272	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.87585	0.153

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	3.04398	0.233

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.70704	0.14
Manapal/WT (break)	3.01869	0.183
Manapal/WT (red)	1.71977	0.126