Tomato Functional Genomics Database (TFGD)

Expression of 1-1-6.3.13.7

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.957	0.77
27DAP/17DAP	1.03431	0.927
39DAP/27DAP	0.87071	0.544
41DAP/39DAP	1.12404	0.859
42DAP/41DAP	1.5695	0.737
43DAP/42DAP	0.92782	0.877
47DAP/43DAP	1.54002	0.576
52DAP/47DAP	0.8814	0.67
57DAP/52DAP	0.98977	0.971

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.89127	0.103
17DAP/reference	1.04539	0.355
27DAP/reference	1.00598	1
39DAP/reference	1.03573	0.377
41DAP/reference	0.92362	0.085
42DAP/reference	0.79077	0.005
43DAP/reference	0.99973	0.924
47DAP/reference	0.93525	0.191
52DAP/reference	0.89582	0.158
57DAP/reference	0.99071	0.639

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.99869	0.801
27DAP/17DAP	0.9946	0.943
39DAP/27DAP	1.18052	0.197
41DAP/39DAP	1.02655	0.914
42DAP/41DAP	1.0367	0.991
43DAP/42DAP	1.06757	0.413
47DAP/43DAP	0.93894	0.577
52DAP/47DAP	1.04929	0.8
57DAP/52DAP	0.96152	0.678
57DAP/7DAP	0.89966	0.186

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.91407	0.27
17DAP/reference	0.83859	0.031
27DAP/reference	0.91282	0.231
39DAP/reference	1.11527	0.538
41DAP/reference	0.95554	0.326
42DAP/reference	0.94466	0.436
43DAP/reference	0.95894	0.385
47DAP/reference	0.85934	0.222
52DAP/reference	0.93444	0.304
57DAP/reference	0.82219	0.056

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.9471	0.518
17DAP/reference	0.87234	0.116
27DAP/reference	0.88668	0.09
39DAP/reference	0.96395	0.455
41DAP/reference	0.9842	0.531
42DAP/reference	0.83778	0.037
43DAP/reference	0.87505	0.152
47DAP/reference	0.8063	0.021
52DAP/reference	0.92132	0.187
57DAP/reference	1.00196	0.789

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.94762	0.422
17DAP/reference	0.89349	0.3
27DAP/reference	0.99711	0.805
39DAP/reference	0.88991	0.122
41DAP/reference	0.94066	0.237
42DAP/reference	0.96013	0.552
43DAP/reference	0.89442	0.171
47DAP/reference	0.83506	0.199
52DAP/reference	0.9364	0.415
57DAP/reference	0.9144	0.288

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.83766	0.807
26DAP/20DAP	1.03481	1
34DAP/26DAP	1.10671	1
51DAP/34DAP	1.12118	0.365
52DAP/51DAP	1.19746	0.186
53DAP/52DAP	1.13519	0.753
55DAP/53DAP	1.01101	1
57DAP/55DAP	0.88585	0.37
62DAP/57DAP	1.26174	1
68DAP/62DAP	0.82176	0.245
68DAP/14DAP	0.53389	0.121

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.15113	0.027

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.78908	0.329
Mature Green Tomato/Ripe Tomato	0.77654	0.165
Immature Eggplant/Mature Eggplant	0.45584
Ripe Pepper/Ripe Tomato	0.51665	0.224
Mature Eggplant/Ripe Tomato	0.57794	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.14936	1
1-1-2/M82	1.04802	1
12-2/M82	0.98197
12-4/M82	0.93816	1
1-3/M82	0.93219
2-1-1/M82	0.89703
2-1/M82	N/A	N/A
2-6/M82	0.66935	1
3-2/M82	1.04447
4-1-1/M82	1.05204	1
4-1/M82	N/A	N/A
4-3-2/M82	0.84348	0.487
4-3/M82	1.20794	1
5-3/M82	1.20652	1
6-2/M82	1.00638	1
6-3/M82	0.92644	1
7-1/M82	N/A	N/A
7-2/M82	N/A	N/A
9-3-2/M82	0.8007

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.89268	0.321
IL2-6/WTpooled	1.29533	0.441
IL7-5/WTpooled	1.87154
IL7-3/WTpooled	0.7494	0.294
IL12-4/WTpooled	1.17991	0.785
IL1-4/WTpooled	0.89562	0.834
WT/WTpooled	1.00969	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	1.05694	0.699

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	N/A	N/A
DC3000/delta hrp 6h	1.02237	1
DC3000/delta hrp 12h	0.94277	1
DC3000/delta hrp 24h	1.16092	0.397

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	N/A	N/A
DC3000 delta B/DC3000 delta AB	1.18478	0.386

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.17127	1
Exp 36h	N/A	N/A
Exp 60h	1.29462	0.283

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

hybridization	ratio	FDR (corrected p value)
self-self	0.98435	1
Var 0h	1.1143	0.421
Var 12h I row2-row1	1.03143	0.736
Var 12h NI row2-row1	1.04698	1
Var 36h I row2-row1	0.9165	1
Var 36h NI row2-row1	1.00626	1
Var 60h I row2-row1	1.05276	1
Var 60h NI row2-row1	0.97717	1
Time course 0hI-0hNI	1.00333	1
Time course 12hI-12hNI	1.08449	0.392
Time course 36hI-36hNI	1.08185	0.089
Time course 60hI-60hNI	1.42291	0.011

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)	0.9608	0.485
transgenic ySAMdc/azygous control (breaker)	0.93808	0.49
transgenic ySAMdc/azygous control (red)	0.89737	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.96277	0.362

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.0059	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.86323	1
Manapal/WT (break)	0.81876	0.333
Manapal/WT (red)	1.20944	0.413