Tomato Functional Genomics Database (TFGD)

Expression of 1-1-8.2.7.13

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.93388	0.586
27DAP/17DAP	0.92068	0.843
39DAP/27DAP	0.98377	0.769
41DAP/39DAP	1.14333	0.85
42DAP/41DAP	1.1967	0.709
43DAP/42DAP	1.03287	1
47DAP/43DAP	1.01295	1
52DAP/47DAP	1.0414	0.964
57DAP/52DAP	1.02959	0.996

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.00835	1
17DAP/reference	0.98131	0.63
27DAP/reference	1.02093	0.759
39DAP/reference	1.01126	0.786
41DAP/reference	0.91123	0.154
42DAP/reference	1.0693	0.125
43DAP/reference	1.0435	0.495
47DAP/reference	0.9838	0.258
52DAP/reference	0.99441	0.668
57DAP/reference	1.07157	0.136

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.9148	0.376
27DAP/17DAP	0.98939	0.854
39DAP/27DAP	0.99758	1
41DAP/39DAP	1.05135	0.439
42DAP/41DAP	1.14491	0.8
43DAP/42DAP	0.95953	0.367
47DAP/43DAP	1.00329	0.973
52DAP/47DAP	1.02716	0.933
57DAP/52DAP	0.93484	0.322
57DAP/7DAP	1.02893	0.249

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.98498	0.613
17DAP/reference	0.90015	0.049
27DAP/reference	0.89447	0.01
39DAP/reference	0.93326	0.126
41DAP/reference	1.08569	0.215
42DAP/reference	1.06267	0.534
43DAP/reference	0.96883	0.403
47DAP/reference	0.99509	1
52DAP/reference	0.97491	0.621
57DAP/reference	1.08523	0.382

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.0186	0.732
17DAP/reference	0.96781	0.279
27DAP/reference	0.97588	0.452
39DAP/reference	0.92232	0.119
41DAP/reference	0.90073	0.01
42DAP/reference	0.9578	0.169
43DAP/reference	0.91768	0.277
47DAP/reference	0.98817	0.574
52DAP/reference	0.91989	0.031
57DAP/reference	0.98049	0.649

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.93163	0.311
17DAP/reference	0.92801	0.109
27DAP/reference	0.89968	0.031
39DAP/reference	0.91451	0.04
41DAP/reference	0.92165	0.07
42DAP/reference	0.91674	0.016
43DAP/reference	0.93322	0.116
47DAP/reference	0.90109	0.103
52DAP/reference	0.88341	0.174
57DAP/reference	0.90731	0.061

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.0131	0.966
26DAP/20DAP	1.009	1
34DAP/26DAP	0.98394	0.98
51DAP/34DAP	1.02753	0.785
52DAP/51DAP	1.03966	0.616
53DAP/52DAP	0.95264
55DAP/53DAP	1.02249	0.82
57DAP/55DAP	1.07952	0.805
62DAP/57DAP	0.82614	0.088
68DAP/62DAP	0.95718	0.863
68DAP/14DAP	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.02118	0.7

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.24793	0.068
Mature Green Tomato/Ripe Tomato	1.32085	0.814
Immature Eggplant/Mature Eggplant	1.5028	0.05
Ripe Pepper/Ripe Tomato	0.92788	1
Mature Eggplant/Ripe Tomato	1.12331	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.93379	0.944
1-1-2/M82	1.07539	1
12-2/M82	0.94383	0.678
12-4/M82	1.01644	1
1-3/M82	0.96152	0.501
2-1-1/M82	0.93544	0.465
2-1/M82	0.83668	0.325
2-6/M82	0.91136	1
3-2/M82	0.97941
4-1-1/M82	1.02985	1
4-1/M82	0.8593
4-3-2/M82	0.91484	0.698
4-3/M82	0.97216	1
5-3/M82	0.9961	1
6-2/M82	0.9486	1
6-3/M82	0.97473	1
7-1/M82	1.01816	1
7-2/M82	0.93492	0.599
9-3-2/M82	1.13486	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.01296	1
IL2-6/WTpooled	1.09421	0.46
IL7-5/WTpooled	1.38397	0.67
IL7-3/WTpooled	0.97478	1
IL12-4/WTpooled	0.80563	0.71
IL1-4/WTpooled	0.785	0.415
WT/WTpooled	1.0905	0.89

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	0.87764	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.02502	0.921
DC3000/delta hrp 6h	1.21965	1
DC3000/delta hrp 12h	0.96966	1
DC3000/delta hrp 24h	1.00485	1

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.11768	0.408
DC3000 delta B/DC3000 delta AB	1.04733	0.498

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	1.01261	1
Var 0h	0.39629	1
Var 12h I row2-row1	1.09707	0.254
Var 12h NI row2-row1	1.01519	1
Var 36h I row2-row1	0.99246	1
Var 36h NI row2-row1	0.9126	0.61
Var 60h I row2-row1	1.15011	1
Var 60h NI row2-row1	1.14018	0.904
Time course 0hI-0hNI	0.92252	0.454
Time course 12hI-12hNI	1.07595	0.409
Time course 36hI-36hNI	1.02685	0.401
Time course 60hI-60hNI	1.10313	0.069

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)	0.8269	0.289
transgenic ySAMdc/azygous control (breaker)	1.07209	1
transgenic ySAMdc/azygous control (red)	1.13699	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.03457	0.247

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.73846	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.95221	1
Manapal/WT (break)	0.98432	1
Manapal/WT (red)	0.59141	0.183