Tomato Functional Genomics Database (TFGD)

Expression of 1-1-8.2.12.19

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.21628	0.575
27DAP/17DAP	0.45267	0.027
39DAP/27DAP	0.66976	0.335
41DAP/39DAP	0.55691	0.049
42DAP/41DAP	0.68832	0.774
43DAP/42DAP	1.28891	0.714
47DAP/43DAP	0.3143	0.049
52DAP/47DAP	1.35192	0.907
57DAP/52DAP	0.75565	0.79

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.72117	0.075
17DAP/reference	0.47326	0.008
27DAP/reference	0.43738	0.015
39DAP/reference	0.4233	0.015
41DAP/reference	0.22315	0.008
42DAP/reference	0.3099	0.001
43DAP/reference	0.1839	0.012
47DAP/reference	0.2533	0.001
52DAP/reference	0.21678	0.013
57DAP/reference	0.24633	0.006

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	2.01718	0.036
27DAP/17DAP	0.67621	0.132
39DAP/27DAP	0.26674	0.029
41DAP/39DAP	1.62471	0.01
42DAP/41DAP	0.78343	0.024
43DAP/42DAP	0.34079	0.022
47DAP/43DAP	0.80817	0.214
52DAP/47DAP	1.00736	0.982
57DAP/52DAP	0.981	0.742
57DAP/7DAP	0.25289	0.219

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.02237	0.999
17DAP/reference	0.62337	0.011
27DAP/reference	0.42283	0.01
39DAP/reference	0.37735	0.011
41DAP/reference	0.25896	0.009
42DAP/reference	0.32105	0.011
43DAP/reference	0.20395	0.009
47DAP/reference	0.25162	0.03
52DAP/reference	0.24788	0.011
57DAP/reference	0.24728	0.006

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.38741	0.007
17DAP/reference	0.42621	0.006
27DAP/reference	0.53534	0.026
39DAP/reference	0.33611	0.01
41DAP/reference	0.39569	0.005
42DAP/reference	0.34916	0.011
43DAP/reference	0.11544	0.001
47DAP/reference	0.20462	0.007
52DAP/reference	0.18597	0.003
57DAP/reference	0.11041	0.002

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.91867	0.023
17DAP/reference	1.79541	0.113
27DAP/reference	1.23575	0.149
39DAP/reference	0.97673	0.544
41DAP/reference	0.57293	0.019
42DAP/reference	0.48584	0.019
43DAP/reference	0.48112	0.02
47DAP/reference	0.27896	0.004
52DAP/reference	0.22212	0.047
57DAP/reference	1.79065	0.187

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.8937	1
26DAP/20DAP	1.10188	0.839
34DAP/26DAP	0.73729	0.131
51DAP/34DAP	0.38275	0.049
52DAP/51DAP	0.99212	1
53DAP/52DAP	0.63675	0.109
55DAP/53DAP	0.57592	0.024
57DAP/55DAP	0.60715	0.02
62DAP/57DAP	1.81132	0.007
68DAP/62DAP	1.36236	0.885
68DAP/14DAP	0.87202	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.27308	0.019

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	2.78726	0.058
Mature Green Tomato/Ripe Tomato	21.1805	0.015
Immature Eggplant/Mature Eggplant	0.51133	0.062
Ripe Pepper/Ripe Tomato	17.6212	0.258
Mature Eggplant/Ripe Tomato	28.0958	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	0.66347
12-2/M82	0.35626
12-4/M82	0.79384	0.282
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	1.57072
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	2.94783	0.467
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	0.959
7-2/M82	1.55513
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.91638	1
IL2-6/WTpooled	1.15114	0.584
IL7-5/WTpooled	0.64629	1
IL7-3/WTpooled	1.022	1
IL12-4/WTpooled	0.89599	1
IL1-4/WTpooled	0.97826	1
WT/WTpooled	0.99185	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	0.95478	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.96813	1
DC3000/delta hrp 6h	0.95343	0.95
DC3000/delta hrp 12h	1.23695	1
DC3000/delta hrp 24h	1.10877	0.411

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.07861
DC3000 delta B/DC3000 delta AB	0.69066	0.117

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.99015	1
Exp 36h	0.86196	0.699
Exp 60h	0.93842	0.754

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

hybridization	ratio	FDR (corrected p value)
self-self	1.06064	1
Var 0h	1.11804	1
Var 12h I row2-row1	1.07097	0.613
Var 12h NI row2-row1	1.02666	1
Var 36h I row2-row1	1.13084	1
Var 36h NI row2-row1	0.91619	0.549
Var 60h I row2-row1	1.51089	0.562
Var 60h NI row2-row1	0.95533	1
Time course 0hI-0hNI	1.0433	0.867
Time course 12hI-12hNI	1.07013	0.668
Time course 36hI-36hNI	1.00432	0.783
Time course 60hI-60hNI	0.87591	0.319

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)	1.16609	0.654
transgenic ySAMdc/azygous control (breaker)	3.14683	0.162
transgenic ySAMdc/azygous control (red)	1.16932	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.47305	0.107

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.94551	0.35

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	18.1768	0.084
Manapal/WT (break)	13.2374	0.123
Manapal/WT (red)	1.4744	1