Tomato Functional Genomics Database (TFGD)

Expression of 1-1-8.2.16.12

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.91562	0.522
27DAP/17DAP	1.37375	0.783
39DAP/27DAP	1.22316	0.504
41DAP/39DAP	1.22119	0.478
42DAP/41DAP	0.97159	1
43DAP/42DAP	1.10044	1
47DAP/43DAP	0.9153	0.696
52DAP/47DAP	1.05284	0.937
57DAP/52DAP	1.10518	0.993

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.54581	0.025
17DAP/reference	0.62254	0.009
27DAP/reference	0.66846	0.012
39DAP/reference	0.65752	0.021
41DAP/reference	0.67624	0.014
42DAP/reference	0.70013	0.001
43DAP/reference	0.75769	0.025
47DAP/reference	0.63624	0.001
52DAP/reference	0.51865	0.012
57DAP/reference	0.70391	0.008

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.84459	0.26
27DAP/17DAP	0.97729	0.887
39DAP/27DAP	1.13314	0.514
41DAP/39DAP	0.99921	1
42DAP/41DAP	1.01485	1
43DAP/42DAP	0.9282	0.321
47DAP/43DAP	1.07335	0.492
52DAP/47DAP	1.05223	0.826
57DAP/52DAP	0.97463	0.768
57DAP/7DAP	1.0814	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.58463	0.043
17DAP/reference	0.60966	0.012
27DAP/reference	0.58755	0.01
39DAP/reference	0.65228	0.011
41DAP/reference	0.60028	0.009
42DAP/reference	0.57279	0.01
43DAP/reference	0.54609	0.01
47DAP/reference	0.73735	0.066
52DAP/reference	0.47539	0.009
57DAP/reference	0.4504	0.006

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.60209	0.01
17DAP/reference	0.53143	0.005
27DAP/reference	0.71071	0.007
39DAP/reference	0.52947	0.009
41DAP/reference	0.6894	0.007
42DAP/reference	0.78041	0.035
43DAP/reference	0.59448	0.004
47DAP/reference	0.72222	0.01
52DAP/reference	0.49093	0.003
57DAP/reference	0.47929	0.003

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.60777	0.03
17DAP/reference	0.69372	0.108
27DAP/reference	0.61322	0.02
39DAP/reference	0.55445	0.006
41DAP/reference	0.68306	0.018
42DAP/reference	0.63466	0.014
43DAP/reference	0.62876	0.016
47DAP/reference	0.63702	0.006
52DAP/reference	0.50477	0.047
57DAP/reference	0.60154	0.017

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.72729	0.44
26DAP/20DAP	1.05529	1
34DAP/26DAP	1.36849	0.819
51DAP/34DAP	1.00873	0.967
52DAP/51DAP	1.00002	1
53DAP/52DAP	1.16293	0.296
55DAP/53DAP	0.94341	0.577
57DAP/55DAP	0.97566	0.828
62DAP/57DAP	1.03339	0.868
68DAP/62DAP	0.88692	0.543
68DAP/14DAP	1.9551	0.131

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.71418	0.037

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.38027	0.078
Mature Green Tomato/Ripe Tomato	2.11336	0.038
Immature Eggplant/Mature Eggplant	1.2739	0.157
Ripe Pepper/Ripe Tomato	1.64491	1
Mature Eggplant/Ripe Tomato	0.60649	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.97578
1-1-2/M82	1.02927	1
12-2/M82	1.02927	1
12-4/M82	0.87521	1
1-3/M82	1.47667	0.479
2-1-1/M82	1.03569	1
2-1/M82	1.06278	1
2-6/M82	1.02369	1
3-2/M82	0.65104
4-1-1/M82	0.85332	1
4-1/M82	0.54867
4-3-2/M82	1.04214	1
4-3/M82	1.08468
5-3/M82	1.4118	0.572
6-2/M82	1.86865
6-3/M82	1.00901	1
7-1/M82	1.20942
7-2/M82	1.33025	1
9-3-2/M82	0.70339

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	2.45229	0.277
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	1.15867	1
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	N/A	N/A
IL1-4/WTpooled	1.05938	1
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	1.12929	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.98478	1
DC3000/delta hrp 6h	0.93948	0.95
DC3000/delta hrp 12h	0.97394	1
DC3000/delta hrp 24h	0.99204	1

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.84437	0.044
DC3000 delta B/DC3000 delta AB	0.96795	0.729

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.19864	1
Exp 36h	1.25224	1
Exp 60h	1.03411	1

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

hybridization	ratio	FDR (corrected p value)
self-self	1.01825	1
Var 0h	1.36952	1
Var 12h I row2-row1	0.81926	0.353
Var 12h NI row2-row1	1.34539	0.281
Var 36h I row2-row1	1.26457	0.601
Var 36h NI row2-row1	0.63131	0.478
Var 60h I row2-row1	1.32143	1
Var 60h NI row2-row1	0.70837	0.431
Time course 0hI-0hNI	1.08174	0.833
Time course 12hI-12hNI	1.02266	1
Time course 36hI-36hNI	1.85121	0.006
Time course 60hI-60hNI	2.31169	0.011

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)	1.06609	0.286
transgenic ySAMdc/azygous control (breaker)	2.91416	0.248
transgenic ySAMdc/azygous control (red)	0.78118	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.0138	0.737

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.75363	0.308

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.73594	1
Manapal/WT (break)	1.47815	1
Manapal/WT (red)	0.59909	0.199