Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.1.1.10

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.13215	0.477
27DAP/17DAP	1.16527	0.809
39DAP/27DAP	1.32502	0.312
41DAP/39DAP	1.11768	0.649
42DAP/41DAP	1.17936	0.786
43DAP/42DAP	1.23393	0.505
47DAP/43DAP	0.8953	0.634
52DAP/47DAP	1.55418	0.338
57DAP/52DAP	1.22371	0.826

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.12346	0.154
17DAP/reference	1.03548	0.178
27DAP/reference	1.03375	0.672
39DAP/reference	1.02839	0.654
41DAP/reference	1.09991	0.312
42DAP/reference	1.24779	0.002
43DAP/reference	1.06997	0.163
47DAP/reference	1.10248	0.023
52DAP/reference	1.04052	0.695
57DAP/reference	1.04826	0.447

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.97263	0.613
27DAP/17DAP	1.06728	0.735
39DAP/27DAP	1.0631	0.483
41DAP/39DAP	1.1175	0.674
42DAP/41DAP	0.95527	0.595
43DAP/42DAP	0.85835	0.027
47DAP/43DAP	0.95359	0.588
52DAP/47DAP	0.99128	0.941
57DAP/52DAP	0.9494	0.514
57DAP/7DAP	1.86202

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.88246	0.168
17DAP/reference	0.91994	0.018
27DAP/reference	0.88006	0.012
39DAP/reference	0.858	0.011
41DAP/reference	0.81345	0.013
42DAP/reference	0.81399	0.01
43DAP/reference	0.84558	0.013
47DAP/reference	0.99305	1
52DAP/reference	0.78854	0.019
57DAP/reference	0.84696	0.006

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.0454	0.35
17DAP/reference	1.15893	0.019
27DAP/reference	1.25094	0.09
39DAP/reference	1.03388	0.806
41DAP/reference	1.02223	1
42DAP/reference	0.98179	0.534
43DAP/reference	1.10246	0.435
47DAP/reference	0.99438	0.695
52DAP/reference	1.01802	0.702
57DAP/reference	1.07541	0.296

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.88736	0.025
17DAP/reference	1.01812	1
27DAP/reference	0.86929	0.041
39DAP/reference	0.90479	0.024
41DAP/reference	0.9136	0.119
42DAP/reference	0.96949	0.287
43DAP/reference	0.95201	0.179
47DAP/reference	1.00607	1
52DAP/reference	1.00797	1
57DAP/reference	1.30399	0.157

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.1135	0.966
26DAP/20DAP	1.02507	1
34DAP/26DAP	1.04801	1
51DAP/34DAP	0.9543	0.66
52DAP/51DAP	0.94023	1
53DAP/52DAP	0.95216	0.75
55DAP/53DAP	1.05185	0.861
57DAP/55DAP	0.94077	0.718
62DAP/57DAP	1.12479	0.047
68DAP/62DAP	1.21239	0.866
68DAP/14DAP	1.69189	0.028

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.2352	0.072

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.95939	0.673
Mature Green Tomato/Ripe Tomato	1.11348	0.299
Immature Eggplant/Mature Eggplant	1.42175	0.051
Ripe Pepper/Ripe Tomato	1.11849	1
Mature Eggplant/Ripe Tomato	1.06542	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.11173	0.742
1-1-2/M82	1.11652	1
12-2/M82	1.02749	1
12-4/M82	0.94488	1
1-3/M82	1.12422	1
2-1-1/M82	1.21763	0.439
2-1/M82	1.70391	0.345
2-6/M82	0.97997	1
3-2/M82	1.03738	0.443
4-1-1/M82	0.82496	0.959
4-1/M82	1.10854
4-3-2/M82	0.85716	1
4-3/M82	0.81747	0.611
5-3/M82	1.30063	0.572
6-2/M82	1.02592	1
6-3/M82	1.01243	1
7-1/M82	0.72506	0.803
7-2/M82	0.9775	0.881
9-3-2/M82	0.94097

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.96584
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	0.95184
WT/WTpooled	N/A	N/A

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	1.10923	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.01241	1
DC3000/delta hrp 6h	0.89782	0.95
DC3000/delta hrp 12h	0.9514	1
DC3000/delta hrp 24h	1.06079	0.633

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.23732	0.042
DC3000 delta B/DC3000 delta AB	1.09081	0.468

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.94194	1
Exp 36h	1.56419	0.693
Exp 60h	1.67037	0.399

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

hybridization	ratio	FDR (corrected p value)
self-self	0.98571	1
Var 0h	0.87938	1
Var 12h I row2-row1	1.09395	0.613
Var 12h NI row2-row1	1.07441	1
Var 36h I row2-row1	1.07934	0.908
Var 36h NI row2-row1	0.8275	0.522
Var 60h I row2-row1	0.93375	0.439
Var 60h NI row2-row1	1.02997	1
Time course 0hI-0hNI	2.19138	0.764
Time course 12hI-12hNI	1.13521	0.233
Time course 36hI-36hNI	1.67564	0.005
Time course 60hI-60hNI	2.63159	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)	0.96512	0.722
transgenic ySAMdc/azygous control (breaker)	1.93143	0.248
transgenic ySAMdc/azygous control (red)	1.22245	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.2717	0.035

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.81739	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.03117	1
Manapal/WT (break)	1.11074	1
Manapal/WT (red)	0.86705	0.315