Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.1.14.12

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.24858	0.997
27DAP/17DAP	0.41987	0.027
39DAP/27DAP	1.21297	0.548
41DAP/39DAP	0.95794	0.772
42DAP/41DAP	0.85396	1
43DAP/42DAP	0.68958	0.705
47DAP/43DAP	1.01311	0.825
52DAP/47DAP	1.0465	0.987
57DAP/52DAP	1.02768	1

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.37249	0.025
17DAP/reference	0.18215	0.007
27DAP/reference	0.16716	0.012
39DAP/reference	0.1461	0.01
41DAP/reference	0.14049	0.009
42DAP/reference	0.22009	0.001
43DAP/reference	0.15891	0.015
47DAP/reference	0.2466	0.001
52DAP/reference	0.195	0.015
57DAP/reference	0.30515	0.007

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.55976	0.033
27DAP/17DAP	0.95726	0.854
39DAP/27DAP	1.01984	0.824
41DAP/39DAP	0.82171	0.265
42DAP/41DAP	0.96485	0.751
43DAP/42DAP	0.79249	0.068
47DAP/43DAP	1.15358	0.756
52DAP/47DAP	1.4075	0.221
57DAP/52DAP	1.19345	0.24
57DAP/7DAP	0.99772	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.23057	0.042
17DAP/reference	0.20505	0.011
27DAP/reference	0.18966	0.01
39DAP/reference	0.1385	0.011
41DAP/reference	0.75916	0.103
42DAP/reference	0.16419	0.01
43DAP/reference	0.12019	0.008
47DAP/reference	0.11833	0.026
52DAP/reference	0.11762	0.009
57DAP/reference	0.10215	0.005

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.20967	0.005
17DAP/reference	0.08476	0.003
27DAP/reference	0.12997	0.005
39DAP/reference	0.1329	0.008
41DAP/reference	0.62196	0.091
42DAP/reference	0.26987	0.014
43DAP/reference	0.14968	0.002
47DAP/reference	0.18095	0.007
52DAP/reference	0.10464	0.003
57DAP/reference	0.1092	0.002

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.25936	0.032
17DAP/reference	0.7854	0.072
27DAP/reference	0.14875	0.02
39DAP/reference	0.12653	0.006
41DAP/reference	0.18631	0.018
42DAP/reference	0.16897	0.014
43DAP/reference	0.12386	0.017
47DAP/reference	0.06166	0.004
52DAP/reference	0.14663	0.047
57DAP/reference	0.19017	0.016

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	2.11632	0.966
26DAP/20DAP	1.79318	0.534
34DAP/26DAP	1.58288	1
51DAP/34DAP	1.49219	0.775
52DAP/51DAP	1.76237	0.033
53DAP/52DAP	0.76018	0.058
55DAP/53DAP	1.23	0.29
57DAP/55DAP	0.62567	0.032
62DAP/57DAP	1.08121	0.902
68DAP/62DAP	1.66688	0.174
68DAP/14DAP	0.96617	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.48106	0.035

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.07832
Mature Green Tomato/Ripe Tomato	10.9855	0.015
Immature Eggplant/Mature Eggplant	18.2148	0.043
Ripe Pepper/Ripe Tomato	N/A	N/A
Mature Eggplant/Ripe Tomato	1.54583	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	N/A	N/A
12-2/M82	N/A	N/A
12-4/M82	N/A	N/A
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	N/A	N/A
3-2/M82	N/A	N/A
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	N/A	N/A
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
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	0.6119	0.243
IL2-6/WTpooled	0.85864	1
IL7-5/WTpooled	0.70568	1
IL7-3/WTpooled	1.10685	1
IL12-4/WTpooled	0.9103	1
IL1-4/WTpooled	0.92385	0.834
WT/WTpooled	0.98753	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	0.64769	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.24529	0.692
DC3000/delta hrp 6h	1.53011	0.777
DC3000/delta hrp 12h	0.12209	1
DC3000/delta hrp 24h	13.9418	0.032

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.8644	0.06
DC3000 delta B/DC3000 delta AB	1.50528	0.081

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	N/A	N/A
Exp 36h	N/A	N/A
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	1.08929	1
Var 0h	1.08341	0.936
Var 12h I row2-row1	0.96302	0.948
Var 12h NI row2-row1	0.81305	0.82
Var 36h I row2-row1	0.71114	1
Var 36h NI row2-row1	1.09908	1
Var 60h I row2-row1	0.8785	0.285
Var 60h NI row2-row1	0.8948	0.63
Time course 0hI-0hNI	1.13022	0.603
Time course 12hI-12hNI	0.91508	0.377
Time course 36hI-36hNI	0.8498	0.023
Time course 60hI-60hNI	0.53446	0.006

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)	0.75996	0.257
transgenic ySAMdc/azygous control (breaker)	1.15149	1
transgenic ySAMdc/azygous control (red)	1.3262	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.95167	0.064

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	2.863	0.277

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.83635	1
Manapal/WT (break)	0.20933	0.333
Manapal/WT (red)	0.83053	0.242