Tomato Functional Genomics Database (TFGD)

Expression of 1-1-8.2.15.1

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.20037	0.827
27DAP/17DAP	1.07053	0.89
39DAP/27DAP	1.31721	0.507
41DAP/39DAP	1.31959	0.63
42DAP/41DAP	1.35208	0.777
43DAP/42DAP	0.98226	0.914
47DAP/43DAP	1.2391	0.756
52DAP/47DAP	1.26336	0.468
57DAP/52DAP	1.80791	0.849

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.9442	0.2
17DAP/reference	1.05831	0.318
27DAP/reference	1.0482	0.384
39DAP/reference	1.07427	0.445
41DAP/reference	1.13562	0.085
42DAP/reference	1.01522	0.995
43DAP/reference	1.06577	0.36
47DAP/reference	1.02554	0.612
52DAP/reference	1.00226	0.636
57DAP/reference	1.04813	0.463

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.23955	0.038
27DAP/17DAP	0.84479	0.312
39DAP/27DAP	1.07412	0.677
41DAP/39DAP	1.09642	0.807
42DAP/41DAP	0.90879	0.481
43DAP/42DAP	0.87835	0.269
47DAP/43DAP	1.14793	0.508
52DAP/47DAP	1.26493	0.498
57DAP/52DAP	1.02433	1
57DAP/7DAP	1.17363	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.00298	0.758
17DAP/reference	1.34464	0.199
27DAP/reference	1.08042	0.804
39DAP/reference	1.19785	0.282
41DAP/reference	1.35049	0.126
42DAP/reference	1.15709	0.534
43DAP/reference	1.03007	0.923
47DAP/reference	1.01497	1
52DAP/reference	1.16954	0.149
57DAP/reference	1.27446	0.147

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.98061	0.736
17DAP/reference	0.97019	0.499
27DAP/reference	0.91072	0.24
39DAP/reference	0.99101	0.603
41DAP/reference	0.98198	0.505
42DAP/reference	1.01403	0.723
43DAP/reference	0.93441	0.263
47DAP/reference	1.06443	0.556
52DAP/reference	1.02412	0.667
57DAP/reference	0.94264	0.298

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.9184	0.311
17DAP/reference	0.96439	0.615
27DAP/reference	1.11757	0.425
39DAP/reference	1.00065	0.889
41DAP/reference	0.9608	0.56
42DAP/reference	1.06158	0.648
43DAP/reference	1.17335	0.432
47DAP/reference	1.11143	0.028
52DAP/reference	1.25844	0.228
57DAP/reference	0.94061	0.394

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.9897	1
26DAP/20DAP	0.68591	0.205
34DAP/26DAP	1.28084	1
51DAP/34DAP	0.70814	0.109
52DAP/51DAP	0.92073	1
53DAP/52DAP	1.08448	0.944
55DAP/53DAP	1.18346	0.781
57DAP/55DAP	1.07607	1
62DAP/57DAP	1.459	0.185
68DAP/62DAP	1.34261	0.392
68DAP/14DAP	0.78503	0.375

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.99935	0.737

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.24687	0.666
Mature Green Tomato/Ripe Tomato	0.32151	0.02
Immature Eggplant/Mature Eggplant	1.01467	0.659
Ripe Pepper/Ripe Tomato	0.78177	1
Mature Eggplant/Ripe Tomato	0.72271	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.87316	0.883
1-1-2/M82	1.01127	1
12-2/M82	0.94933	0.955
12-4/M82	0.99119	1
1-3/M82	0.84858	0.441
2-1-1/M82	0.97834	1
2-1/M82	N/A	N/A
2-6/M82	0.95861	1
3-2/M82	0.95549
4-1-1/M82	0.98127	1
4-1/M82	N/A	N/A
4-3-2/M82	1.12911	1
4-3/M82	N/A	N/A
5-3/M82	0.96273	1
6-2/M82	0.90207	1
6-3/M82	0.95605	1
7-1/M82	1.29677	1
7-2/M82	1.05913	1
9-3-2/M82	1.12035	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.86166	0.321
IL2-6/WTpooled	0.87393	0.358
IL7-5/WTpooled	0.9646	1
IL7-3/WTpooled	0.74194	0.31
IL12-4/WTpooled	0.61254	0.458
IL1-4/WTpooled	0.93963	0.699
WT/WTpooled	0.97345	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	0.9605	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.00901	1
DC3000/delta hrp 6h	0.95885	0.95
DC3000/delta hrp 12h	0.97287	1
DC3000/delta hrp 24h	0.94744	0.585

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.97555
DC3000 delta B/DC3000 delta AB	0.69388	0.058

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.9395	1
Exp 36h	1.12828	0.693
Exp 60h	0.78856	0.32

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

hybridization	ratio	FDR (corrected p value)
self-self	1.02667	1
Var 0h	0.74638	0.933
Var 12h I row2-row1	0.83194	0.418
Var 12h NI row2-row1	0.99758	1
Var 36h I row2-row1	0.85232	1
Var 36h NI row2-row1	1.21359	0.482
Var 60h I row2-row1	1.07483	1
Var 60h NI row2-row1	1.0846	0.904
Time course 0hI-0hNI	1.05646	0.833
Time course 12hI-12hNI	0.98995	0.984
Time course 36hI-36hNI	0.95368	0.403
Time course 60hI-60hNI	0.36498	0.006

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)	1.08884	0.384
transgenic ySAMdc/azygous control (breaker)	1.02616	1
transgenic ySAMdc/azygous control (red)	1.06773	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.989	0.568

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.50483	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.67048	0.083
Manapal/WT (break)	1.2188	1
Manapal/WT (red)	1.4375	0.142