Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.4.13.20

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.94012	0.64
27DAP/17DAP	1.15139	0.833
39DAP/27DAP	1.10077	0.841
41DAP/39DAP	0.88796	0.536
42DAP/41DAP	1.09534	0.974
43DAP/42DAP	0.99992	0.937
47DAP/43DAP	1.22178	0.369
52DAP/47DAP	0.81513	0.489
57DAP/52DAP	0.99394	0.983

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.00557	1
17DAP/reference	0.99143	0.737
27DAP/reference	1.00355	0.966
39DAP/reference	0.95296	0.267
41DAP/reference	0.99657	1
42DAP/reference	0.99446	0.501
43DAP/reference	0.98896	0.805
47DAP/reference	0.96678	0.127
52DAP/reference	1.00742	0.791
57DAP/reference	1.01132	0.984

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.97875	0.697
27DAP/17DAP	0.97974	0.878
39DAP/27DAP	0.97567	0.648
41DAP/39DAP	1.00455	1
42DAP/41DAP	1.01391	0.947
43DAP/42DAP	0.98992	0.854
47DAP/43DAP	0.98896	0.93
52DAP/47DAP	0.97597	0.837
57DAP/52DAP	0.99813	0.902
57DAP/7DAP	0.95976	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.01029	1
17DAP/reference	0.96052	0.338
27DAP/reference	1.0462	0.453
39DAP/reference	0.99538	0.64
41DAP/reference	1.0346	0.701
42DAP/reference	0.97503	0.371
43DAP/reference	0.95889	0.23
47DAP/reference	0.94492	0.383
52DAP/reference	0.96546	0.523
57DAP/reference	0.95086	0.302

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.94405	0.214
17DAP/reference	0.94926	0.164
27DAP/reference	0.97227	0.501
39DAP/reference	1.06154	0.556
41DAP/reference	1.07652	0.344
42DAP/reference	0.9756	0.433
43DAP/reference	0.97702	0.561
47DAP/reference	1.0196	0.658
52DAP/reference	0.98048	0.433
57DAP/reference	1.05382	0.609

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.06431	0.397
17DAP/reference	1.06791	0.237
27DAP/reference	0.99387	0.763
39DAP/reference	1.01031	0.912
41DAP/reference	0.9642	0.209
42DAP/reference	0.91872	0.087
43DAP/reference	0.93621	0.216
47DAP/reference	1.02973	0.704
52DAP/reference	1.0095	0.952
57DAP/reference	1.03992	0.648

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.96423
26DAP/20DAP	1.05474	0.962
34DAP/26DAP	0.9859	1
51DAP/34DAP	0.97306	0.785
52DAP/51DAP	1.01897	0.836
53DAP/52DAP	1.04766	0.783
55DAP/53DAP	0.9942	0.894
57DAP/55DAP	1.01164	0.944
62DAP/57DAP	0.92296	0.28
68DAP/62DAP	1.0211	1
68DAP/14DAP	1.28721	0.17

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.94611	0.422

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.9931	0.783
Mature Green Tomato/Ripe Tomato	1.29647	0.478
Immature Eggplant/Mature Eggplant	2.65036	0.05
Ripe Pepper/Ripe Tomato	0.46445	0.293
Mature Eggplant/Ripe Tomato	3.56275	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.97179	0.944
1-1-2/M82	0.9583	0.958
12-2/M82	0.94319	0.955
12-4/M82	1.07341	1
1-3/M82	0.99499	1
2-1-1/M82	0.86747	0.465
2-1/M82	1.03843	1
2-6/M82	0.98205	1
3-2/M82	0.99247	1
4-1-1/M82	0.99656	1
4-1/M82	1.27318	0.853
4-3-2/M82	0.79644	0.487
4-3/M82	0.94022	0.72
5-3/M82	0.96114	1
6-2/M82	0.97222	1
6-3/M82	1.03157	1
7-1/M82	1.05431	0.598
7-2/M82	0.81563	0.881
9-3-2/M82	0.9328

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	1.14703	0.659
IL7-5/WTpooled	1.02309
IL7-3/WTpooled	1.00164	1
IL12-4/WTpooled	1.03375	0.785
IL1-4/WTpooled	0.87649	0.834
WT/WTpooled	0.96176	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	1.18871	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.04308	0.921
DC3000/delta hrp 6h	1.24852	1
DC3000/delta hrp 12h	0.99779	1
DC3000/delta hrp 24h	1.03711	0.633

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.12907	0.055
DC3000 delta B/DC3000 delta AB	1.08703	0.358

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.04376	1
Exp 36h	1.36954	0.489
Exp 60h	1.20722	0.399

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

hybridization	ratio	FDR (corrected p value)
self-self	1.00698	1
Var 0h	1.02949	0.98
Var 12h I row2-row1	1.39863	0.283
Var 12h NI row2-row1	1.1226	0.34
Var 36h I row2-row1	0.71002	0.805
Var 36h NI row2-row1	1.21039	1
Var 60h I row2-row1	0.83117	0.285
Var 60h NI row2-row1	1.04679	0.904
Time course 0hI-0hNI	0.99231	1
Time course 12hI-12hNI	1.07902	0.567
Time course 36hI-36hNI	1.22584	0.019
Time course 60hI-60hNI	3.7938	0.008

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)	1.02969	0.612
transgenic ySAMdc/azygous control (breaker)	0.69977	0.173
transgenic ySAMdc/azygous control (red)	1.29665	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.95595	0.313

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.95303	0.789

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.24759	1
Manapal/WT (break)	0.9477	1
Manapal/WT (red)	1.1379	1