Tomato Functional Genomics Database (TFGD)

Expression of 1-1-5.3.7.20

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.8947	0.568
27DAP/17DAP	1.32433	0.778
39DAP/27DAP	1.36076	0.176
41DAP/39DAP	0.81964	0.499
42DAP/41DAP	0.99492	1
43DAP/42DAP	1.31735	0.629
47DAP/43DAP	1.60639	0.52
52DAP/47DAP	1.1825	0.821
57DAP/52DAP	1.23773	1

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.79555	0.059
17DAP/reference	0.89459	0.169
27DAP/reference	0.95166	0.457
39DAP/reference	0.90312	0.276
41DAP/reference	0.81282	0.016
42DAP/reference	0.89904	0.072
43DAP/reference	1.061	0.678
47DAP/reference	0.88961	0.014
52DAP/reference	0.9909	0.564
57DAP/reference	1.13009	0.041

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.93914	0.454
27DAP/17DAP	1.20296	0.112
39DAP/27DAP	0.96287	0.754
41DAP/39DAP	0.96064	0.849
42DAP/41DAP	1.06144	0.753
43DAP/42DAP	1.10879	0.513
47DAP/43DAP	1.11076	0.713
52DAP/47DAP	0.93673	0.726
57DAP/52DAP	1.14714	0.389
57DAP/7DAP	0.99942	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.89298	0.246
17DAP/reference	0.98197	0.518
27DAP/reference	1.0548	0.664
39DAP/reference	0.96529	0.474
41DAP/reference	1.00993	0.778
42DAP/reference	0.87102	0.031
43DAP/reference	0.80387	0.252
47DAP/reference	0.82447	0.504
52DAP/reference	1.22131	0.062
57DAP/reference	1.02883	1

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.03147	0.894
17DAP/reference	0.88658	0.164
27DAP/reference	0.7388	0.044
39DAP/reference	0.78385	0.069
41DAP/reference	1.00745	0.584
42DAP/reference	0.88507	0.15
43DAP/reference	0.75827	0.186
47DAP/reference	0.78165	0.01
52DAP/reference	0.91848	0.06
57DAP/reference	0.8228	0.05

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.20708	0.251
17DAP/reference	1.04169	0.72
27DAP/reference	1.0313	0.883
39DAP/reference	0.88009	0.393
41DAP/reference	1.33328	0.104
42DAP/reference	1.08545	0.836
43DAP/reference	1.00076	0.66
47DAP/reference	0.97506	0.478
52DAP/reference	0.92887	0.455
57DAP/reference	1.01434	0.842

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.71396	0.42
26DAP/20DAP	1.36541	0.281
34DAP/26DAP	0.70622	0.519
51DAP/34DAP	1.3329	0.177
52DAP/51DAP	0.80376	1
53DAP/52DAP	1.18181	0.565
55DAP/53DAP	0.98617	0.82
57DAP/55DAP	0.85006	0.37
62DAP/57DAP	0.8166	0.28
68DAP/62DAP	1.09626	0.869
68DAP/14DAP	1.03417	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.98047	0.737

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	2.18268	0.577
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	N/A	N/A
Mature Eggplant/Ripe Tomato	1.06996	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	1.07862	1
12-2/M82	0.92994
12-4/M82	1.04875	1
1-3/M82	1.83237
2-1-1/M82	N/A	N/A
2-1/M82	N/A	N/A
2-6/M82	N/A	N/A
3-2/M82	2.54688
4-1-1/M82	N/A	N/A
4-1/M82	N/A	N/A
4-3-2/M82	N/A	N/A
4-3/M82	N/A	N/A
5-3/M82	1.66638	1
6-2/M82	5.5956	0.253
6-3/M82	0.7643	0.473
7-1/M82	1.10886	1
7-2/M82	N/A	N/A
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	N/A	N/A
IL1-4/WTpooled	N/A	N/A
WT/WTpooled	0.59003

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	1.1047	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.0378	0.921
DC3000/delta hrp 6h	1.27723	0.95
DC3000/delta hrp 12h	0.94626	1
DC3000/delta hrp 24h	1.70882	0.028

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	1.02121	1

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	N/A	N/A
Exp 36h	0.93222	0.943
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	1.02531	1
Var 0h	0.81102	0.457
Var 12h I row2-row1	1.12156	0.379
Var 12h NI row2-row1	1.12773	0.649
Var 36h I row2-row1	1.22526	1
Var 36h NI row2-row1	3.92398	1
Var 60h I row2-row1	0.93612	0.582
Var 60h NI row2-row1	0.98832	1
Time course 0hI-0hNI	1.01539	1
Time course 12hI-12hNI	1.05739	0.603
Time course 36hI-36hNI	0.97239	0.468
Time course 60hI-60hNI	0.80773	0.047

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)	1.03947	0.511
transgenic ySAMdc/azygous control (breaker)	1.05598	1
transgenic ySAMdc/azygous control (red)	1.24543	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.98834	0.534

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.86537	0.284

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.80417	1
Manapal/WT (break)	0.8247	0.299
Manapal/WT (red)	0.41799	0.229