Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.2.6.8

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.23896	0.602
27DAP/17DAP	0.97078	0.947
39DAP/27DAP	1.1657	0.833
41DAP/39DAP	0.88162	0.518
42DAP/41DAP	1.35514	0.307
43DAP/42DAP	0.97679	0.925
47DAP/43DAP	1.28333	0.321
52DAP/47DAP	0.79336	0.5
57DAP/52DAP	1.17883	0.912

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.92415	0.3
17DAP/reference	0.80123	0.057
27DAP/reference	0.98472	0.741
39DAP/reference	1.02363	0.679
41DAP/reference	0.91823	0.154
42DAP/reference	1.00787	0.688
43DAP/reference	1.00283	0.882
47DAP/reference	1.14215	0.101
52DAP/reference	1.16903	0.354
57DAP/reference	1.30693	0.01

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.42261	0.063
27DAP/17DAP	1.05315	0.932
39DAP/27DAP	0.99983	1
41DAP/39DAP	1.01836	1
42DAP/41DAP	1.08396	0.753
43DAP/42DAP	1.05548	0.664
47DAP/43DAP	0.92643	0.597
52DAP/47DAP	0.97826	0.905
57DAP/52DAP	0.96405	0.732
57DAP/7DAP	0.4705	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.9126	0.183
17DAP/reference	1.01413	1
27DAP/reference	1.11733	0.246
39DAP/reference	0.9521	0.411
41DAP/reference	1.12652	0.539
42DAP/reference	0.89004	0.235
43DAP/reference	0.9084	0.527
47DAP/reference	1.16452	0.13
52DAP/reference	1.26515	0.121
57DAP/reference	1.13841	0.117

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.8344	0.214
17DAP/reference	0.91306	0.149
27DAP/reference	1.12663	0.178
39DAP/reference	1.0606	0.725
41DAP/reference	1.34237	0.03
42DAP/reference	1.09303	0.38
43DAP/reference	1.08029	0.347
47DAP/reference	1.07377	0.544
52DAP/reference	0.96139	0.302
57DAP/reference	1.04383	0.567

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.86867	0.135
17DAP/reference	0.92052	0.433
27DAP/reference	0.84088	0.14
39DAP/reference	3.29771	0.353
41DAP/reference	1.24563	0.181
42DAP/reference	1.09443	0.54
43DAP/reference	1.28391	0.098
47DAP/reference	1.06761	0.61
52DAP/reference	1.26377	0.144
57DAP/reference	1.3449	0.056

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.79858	0.966
26DAP/20DAP	1.07443	1
34DAP/26DAP	1.22154	0.304
51DAP/34DAP	1.09436	0.719
52DAP/51DAP	0.81457	1
53DAP/52DAP	1.20027	0.565
55DAP/53DAP	0.85669	0.13
57DAP/55DAP	1.43526	0.249
62DAP/57DAP	1.12636	1
68DAP/62DAP	1.18506	0.707
68DAP/14DAP	1.39054	0.091

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.8571	0.224

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.26661	0.075
Mature Green Tomato/Ripe Tomato	0.84649	0.317
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	1.38506	1
Mature Eggplant/Ripe Tomato	0.92243	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.04024	0.742
1-1-2/M82	1.15959	1
12-2/M82	N/A	N/A
12-4/M82	0.8808	1
1-3/M82	N/A	N/A
2-1-1/M82	N/A	N/A
2-1/M82	N/A	N/A
2-6/M82	1.01833	1
3-2/M82	1.23213
4-1-1/M82	0.80308
4-1/M82	N/A	N/A
4-3-2/M82	1.30708
4-3/M82	0.91253
5-3/M82	0.99134	1
6-2/M82	N/A	N/A
6-3/M82	0.99165
7-1/M82	0.92285
7-2/M82	1.14479	1
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.40419
IL2-6/WTpooled	1.06046	0.788
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.12981	1
IL12-4/WTpooled	0.9509	0.566
IL1-4/WTpooled	0.97901	1
WT/WTpooled	0.97714	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	1.09386	0.222

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.9803	1
DC3000/delta hrp 6h	1.05736	0.609
DC3000/delta hrp 12h	0.93745	1
DC3000/delta hrp 24h	1.18923	0.09

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	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.90949	1
Exp 36h	0.92492	0.879
Exp 60h	0.88897	0.586

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

hybridization	ratio	FDR (corrected p value)
self-self	0.64326
Var 0h	0.93608	1
Var 12h I row2-row1	0.94268	0.77
Var 12h NI row2-row1	1.13594	0.34
Var 36h I row2-row1	1.31498	0.601
Var 36h NI row2-row1	0.77728	0.706
Var 60h I row2-row1	0.91197	0.832
Var 60h NI row2-row1	0.86192	0.38
Time course 0hI-0hNI	0.96313	0.771
Time course 12hI-12hNI	0.90887	0.166
Time course 36hI-36hNI	0.98894	0.654
Time course 60hI-60hNI	0.85927	0.081

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)	0.93369	0.286
transgenic ySAMdc/azygous control (breaker)	0.6731	0.139
transgenic ySAMdc/azygous control (red)	1.03713	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.99768	0.806

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.93676	0.59

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.86512	0.307
Manapal/WT (break)	1.92912	0.14
Manapal/WT (red)	1.34788	0.222