Tomato Functional Genomics Database (TFGD)

Expression of 1-1-8.2.17.11

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.83588	0.347
27DAP/17DAP	1.06021	0.88
39DAP/27DAP	1.04162	1
41DAP/39DAP	0.87546	0.478
42DAP/41DAP	1.07644	1
43DAP/42DAP	1.16987	0.976
47DAP/43DAP	1.17554	0.576
52DAP/47DAP	0.93614	0.793
57DAP/52DAP	1.19084	0.977

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.24392	0.021
17DAP/reference	1.09703	0.369
27DAP/reference	1.24264	0.067
39DAP/reference	1.03572	0.857
41DAP/reference	1.28068	0.203
42DAP/reference	1.26149	0.041
43DAP/reference	1.15314	0.617
47DAP/reference	1.17485	0.046
52DAP/reference	1.89518	0.008
57DAP/reference	1.42982	0.028

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.14854	0.365
27DAP/17DAP	0.93854	0.206
39DAP/27DAP	0.91178	0.218
41DAP/39DAP	1.07299	0.656
42DAP/41DAP	0.98478	0.841
43DAP/42DAP	0.90368	0.143
47DAP/43DAP	0.98619	0.947
52DAP/47DAP	1.01559	0.991
57DAP/52DAP	1.05001	0.818
57DAP/7DAP	0.9537	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.92519	0.361
17DAP/reference	0.8071	0.018
27DAP/reference	1.00174	0.748
39DAP/reference	0.72571	0.015
41DAP/reference	0.73756	0.039
42DAP/reference	0.83889	0.046
43DAP/reference	0.88779	0.031
47DAP/reference	1.03753	0.901
52DAP/reference	0.82943	0.083
57DAP/reference	0.72941	0.013

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.19287	0.246
17DAP/reference	1.05448	0.806
27DAP/reference	1.10552	0.573
39DAP/reference	1.17142	0.272
41DAP/reference	1.45624	0.007
42DAP/reference	1.35318	0.102
43DAP/reference	1.26464	0.719
47DAP/reference	1.05748	0.712
52DAP/reference	1.12985	0.667
57DAP/reference	1.0319	0.887

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.89505	0.214
17DAP/reference	0.95466	0.56
27DAP/reference	0.82038	0.089
39DAP/reference	0.95918	0.43
41DAP/reference	0.84855	0.04
42DAP/reference	1.03983	0.994
43DAP/reference	0.9607	0.468
47DAP/reference	0.90365	0.259
52DAP/reference	0.88664	0.424
57DAP/reference	1.37397	0.268

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.10637	0.966
26DAP/20DAP	4.571	0.409
34DAP/26DAP	1.32732	0.819
51DAP/34DAP	1.03062	0.869
52DAP/51DAP	1.18651	0.439
53DAP/52DAP	1.31542	0.552
55DAP/53DAP	1.27153	0.566
57DAP/55DAP	0.95157	0.736
62DAP/57DAP	1.02103	1
68DAP/62DAP	2.04431	0.035
68DAP/14DAP	2.04148	0.084

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.7161	0.015

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	1.04087	0.69
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	0.6855	1
Mature Eggplant/Ripe Tomato	0.84987	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.05989	1
1-1-2/M82	1.28043	1
12-2/M82	0.81464	0.74
12-4/M82	1.12191	1
1-3/M82	0.58673	0.378
2-1-1/M82	1.44376	0.439
2-1/M82	N/A	N/A
2-6/M82	1.08146
3-2/M82	0.80303
4-1-1/M82	N/A	N/A
4-1/M82	1.16409	0.429
4-3-2/M82	1.15216	1
4-3/M82	1.20342
5-3/M82	1.08504	1
6-2/M82	0.92088	1
6-3/M82	0.8265	1
7-1/M82	N/A	N/A
7-2/M82	N/A	N/A
9-3-2/M82	1.37141	0.182

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.0054	1
IL2-6/WTpooled	0.9453	1
IL7-5/WTpooled	1.48647
IL7-3/WTpooled	1.05301	1
IL12-4/WTpooled	1.02293	0.891
IL1-4/WTpooled	1.64006	1
WT/WTpooled	1.02317	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	0.79064	0.209

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.02886	0.921
DC3000/delta hrp 6h	0.4246
DC3000/delta hrp 12h	1.36068	1
DC3000/delta hrp 24h	1.02543	0.743

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.13247
DC3000 delta B/DC3000 delta AB	0.86336	0.152

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.16148	1
Exp 36h	0.71134	0.256
Exp 60h	1.01659	1

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

hybridization	ratio	FDR (corrected p value)
self-self	0.94854	1
Var 0h	0.74036	1
Var 12h I row2-row1	0.92044	0.338
Var 12h NI row2-row1	1.15155	1
Var 36h I row2-row1	1.022	0.908
Var 36h NI row2-row1	0.89053	0.645
Var 60h I row2-row1	1.03331	0.562
Var 60h NI row2-row1	1.00687	1
Time course 0hI-0hNI	1.01552	0.867
Time course 12hI-12hNI	0.95085	0.698
Time course 36hI-36hNI	0.95807	0.484
Time course 60hI-60hNI	0.95575	0.319

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)	1.03442	0.699
transgenic ySAMdc/azygous control (breaker)	1.0765	1
transgenic ySAMdc/azygous control (red)	1.02528	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.86832	0.255

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.07253	1
Manapal/WT (break)	1.00879	1
Manapal/WT (red)	1.00348	1