Tomato Functional Genomics Database (TFGD)

Expression of 1-1-4.4.11.20

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.02372	0.997
27DAP/17DAP	1.14562	0.857
39DAP/27DAP	1.43143	0.493
41DAP/39DAP	1.06617	0.844
42DAP/41DAP	1.09817	1
43DAP/42DAP	1.0055	0.937
47DAP/43DAP	1.39053	0.609
52DAP/47DAP	1.15605	0.769
57DAP/52DAP	0.97545	0.971

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.91168	0.231
17DAP/reference	1.18668	0.057
27DAP/reference	1.27683	0.048
39DAP/reference	1.36494	0.125
41DAP/reference	1.63514	0.009
42DAP/reference	1.02889	1
43DAP/reference	1.0109	0.899
47DAP/reference	0.93614	0.174
52DAP/reference	1.00397	0.749
57DAP/reference	0.98087	0.553

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	2.56293	0.06
27DAP/17DAP	0.86918	0.446
39DAP/27DAP	1.06323	0.832
41DAP/39DAP	1.25627	0.656
42DAP/41DAP	1.17425	0.947
43DAP/42DAP	1.15993	0.585
47DAP/43DAP	0.91846	0.637
52DAP/47DAP	1.06516	0.826
57DAP/52DAP	1.22383	0.594
57DAP/7DAP	0.9801	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.1376	0.945
17DAP/reference	0.78647	0.013
27DAP/reference	0.90312	0.048
39DAP/reference	0.79924	0.011
41DAP/reference	0.81018	0.022
42DAP/reference	0.80613	0.013
43DAP/reference	0.72363	0.012
47DAP/reference	0.82473	0.128
52DAP/reference	0.70144	0.012
57DAP/reference	0.77154	0.018

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.30895	0.063
17DAP/reference	1.18187	0.139
27DAP/reference	1.26088	0.136
39DAP/reference	1.14792	0.042
41DAP/reference	0.94436	0.291
42DAP/reference	1.09081	0.5
43DAP/reference	1.89891	0.035
47DAP/reference	1.2036	0.043
52DAP/reference	1.33855	0.014
57DAP/reference	1.33245	0.026

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.81044	0.044
17DAP/reference	0.95445	0.571
27DAP/reference	0.78809	0.043
39DAP/reference	0.89885	0.199
41DAP/reference	1.00476	0.754
42DAP/reference	0.88724	0.22
43DAP/reference	0.83854	0.12
47DAP/reference	1.27582	0.012
52DAP/reference	1.00455	0.946
57DAP/reference	1.13057	0.522

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.0726	0.966
26DAP/20DAP	0.83611
34DAP/26DAP	1.50454	0.819
51DAP/34DAP	0.99471	0.779
52DAP/51DAP	1.23928	0.377
53DAP/52DAP	1.02921	0.99
55DAP/53DAP	1.09927	0.782
57DAP/55DAP	0.9545	0.78
62DAP/57DAP	0.97613	0.994
68DAP/62DAP	1.11843	1
68DAP/14DAP	0.92961

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.72186	0.108

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	N/A	N/A
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	0.40921
Mature Eggplant/Ripe Tomato	N/A	N/A

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	0.82414	1
3-2/M82	0.90698
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	0.88163	0.321
IL2-6/WTpooled	1.04803	0.788
IL7-5/WTpooled	0.5995
IL7-3/WTpooled	0.97181	1
IL12-4/WTpooled	0.77042	0.71
IL1-4/WTpooled	1.25296	1
WT/WTpooled	0.95503	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	1.01583

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.13134	0.921
DC3000/delta hrp 6h	N/A	N/A
DC3000/delta hrp 12h	0.73906	1
DC3000/delta hrp 24h	0.92841	0.564

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	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	1.19556	1
Var 0h	1.06454	0.98
Var 12h I row2-row1	1.08746	0.692
Var 12h NI row2-row1	N/A	N/A
Var 36h I row2-row1	0.9122	0.805
Var 36h NI row2-row1	1.19098
Var 60h I row2-row1	1.09616
Var 60h NI row2-row1	0.44842	1
Time course 0hI-0hNI	0.8884	0.799
Time course 12hI-12hNI	1.03969	0.788
Time course 36hI-36hNI	0.77817	0.162
Time course 60hI-60hNI	0.97699	0.646

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)	1.17107	0.482
transgenic ySAMdc/azygous control (breaker)	0.90749	1
transgenic ySAMdc/azygous control (red)	1.05304	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.02188	0.587

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.08651	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.01067	1
Manapal/WT (break)	1.39386	0.381
Manapal/WT (red)	1.18769	0.413