Tomato Functional Genomics Database (TFGD)

Expression of 1-1-4.2.2.13

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.94396	0.689
27DAP/17DAP	0.97506	0.959
39DAP/27DAP	1.48842	0.189
41DAP/39DAP	0.7655	0.252
42DAP/41DAP	0.98703	1
43DAP/42DAP	0.87097	0.799
47DAP/43DAP	0.87162	0.584
52DAP/47DAP	1.28913	0.96
57DAP/52DAP	1.26483	0.918

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.06648	0.567
17DAP/reference	1.09883	0.161
27DAP/reference	1.1122	0.52
39DAP/reference	1.1963	0.197
41DAP/reference	1.04097	0.714
42DAP/reference	1.45191	0.001
43DAP/reference	1.46778	0.007
47DAP/reference	1.55799	0.001
52DAP/reference	0.93458	0.275
57DAP/reference	1.10391	0.094

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.92587	0.415
27DAP/17DAP	1.11158	0.74
39DAP/27DAP	0.8523	0.227
41DAP/39DAP	1.14048	0.817
42DAP/41DAP	1.11292	0.694
43DAP/42DAP	0.86982	0.149
47DAP/43DAP	0.95026	0.656
52DAP/47DAP	0.84275	0.309
57DAP/52DAP	0.97195	0.695
57DAP/7DAP	0.87025	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.15135	0.189
17DAP/reference	0.99092	0.599
27DAP/reference	0.87055	0.109
39DAP/reference	1.09288	0.175
41DAP/reference	0.92116	0.174
42DAP/reference	1.07426	0.889
43DAP/reference	1.25104	0.2
47DAP/reference	1.55257	0.079
52DAP/reference	1.31721	0.105
57DAP/reference	1.09648	0.746

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.99936	0.907
17DAP/reference	1.35843	0.009
27DAP/reference	1.4971	0.012
39DAP/reference	1.46053	0.021
41DAP/reference	1.37526	0.008
42DAP/reference	1.27508	0.062
43DAP/reference	1.12407	0.854
47DAP/reference	1.21464	0.084
52DAP/reference	1.09414	0.259
57DAP/reference	1.04805	0.567

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.04792	0.575
17DAP/reference	1.01546	0.977
27DAP/reference	0.76472	0.092
39DAP/reference	0.85518	0.122
41DAP/reference	1.00541	1
42DAP/reference	1.13014	0.529
43DAP/reference	1.44174	0.168
47DAP/reference	1.56017	0.009
52DAP/reference	1.05149	0.928
57DAP/reference	1.94049	0.012

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.11954	0.966
26DAP/20DAP	1.35402	0.246
34DAP/26DAP	0.81503	0.431
51DAP/34DAP	1.25232	0.387
52DAP/51DAP	0.91195	1
53DAP/52DAP	1.04495	0.944
55DAP/53DAP	0.93426	0.761
57DAP/55DAP	1.23244	0.666
62DAP/57DAP	1.0228	0.935
68DAP/62DAP	0.86323	0.7
68DAP/14DAP	0.84865	0.075

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.43885	0.014

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.1006	0.176
Mature Green Tomato/Ripe Tomato	1.79981	0.064
Immature Eggplant/Mature Eggplant	1.09105	0.288
Ripe Pepper/Ripe Tomato	8.52075	1
Mature Eggplant/Ripe Tomato	4.41766	0.373

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.03366
1-1-2/M82	N/A	N/A
12-2/M82	N/A	N/A
12-4/M82	1.13995
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	0.94941
3-2/M82	N/A	N/A
4-1-1/M82	N/A	N/A
4-1/M82	1.21823
4-3-2/M82	N/A	N/A
4-3/M82	N/A	N/A
5-3/M82	1.07527	1
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	0.83027
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	0.9823	1
IL12-4/WTpooled	1.11106	0.839
IL1-4/WTpooled	1.1452
WT/WTpooled	0.97492	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	1.095	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.03905	0.921
DC3000/delta hrp 6h	0.9275	0.95
DC3000/delta hrp 12h	0.98449	1
DC3000/delta hrp 24h	0.35853	0.034

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.00691	1
DC3000 delta B/DC3000 delta AB	0.85556	0.288

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.01284	1
Exp 36h	0.99096	1
Exp 60h	0.92216	0.754

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

hybridization	ratio	FDR (corrected p value)
self-self	0.98417	1
Var 0h	0.88442	1
Var 12h I row2-row1	0.92915	0.77
Var 12h NI row2-row1	1.22046	0.34
Var 36h I row2-row1	0.98654	1
Var 36h NI row2-row1	1.08037	1
Var 60h I row2-row1	1.00115	1
Var 60h NI row2-row1	0.86947	0.818
Time course 0hI-0hNI	0.91659	0.359
Time course 12hI-12hNI	0.98587	0.935
Time course 36hI-36hNI	1.17264	0.128
Time course 60hI-60hNI	0.88055	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)	0.99527	0.662
transgenic ySAMdc/azygous control (breaker)	1.08193	1
transgenic ySAMdc/azygous control (red)	1.12365	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.12078	0.135

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.78755	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.253	0.307
Manapal/WT (break)	1.65356	0.14
Manapal/WT (red)	1.04148	1