Tomato Functional Genomics Database (TFGD)

Expression of 1-1-4.3.20.14

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.74834	0.131
27DAP/17DAP	1.28288	0.801
39DAP/27DAP	0.78773	0.482
41DAP/39DAP	1.26567	0.339
42DAP/41DAP	1.24404	0.595
43DAP/42DAP	1.22243	0.768
47DAP/43DAP	1.28932	0.4
52DAP/47DAP	1.18084	0.702
57DAP/52DAP	0.93471	0.919

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.79169	0.033
17DAP/reference	0.90283	0.169
27DAP/reference	0.95749	0.406
39DAP/reference	0.9396	0.381
41DAP/reference	0.83764	0.154
42DAP/reference	0.83789	0.004
43DAP/reference	0.84279	0.058
47DAP/reference	0.88294	0.018
52DAP/reference	0.97596	0.475
57DAP/reference	1.03068	0.744

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.16368	0.398
27DAP/17DAP	1.0881	0.761
39DAP/27DAP	1.14701	0.496
41DAP/39DAP	1.1053	0.88
42DAP/41DAP	0.97252	0.746
43DAP/42DAP	0.88356	0.206
47DAP/43DAP	0.86929	0.569
52DAP/47DAP	1.44095	0.186
57DAP/52DAP	1.47496	0.476
57DAP/7DAP	1.71953	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.15473
17DAP/reference	2.11703	0.007
27DAP/reference	2.53073	0.006
39DAP/reference	2.15749	0.009
41DAP/reference	1.58976	0.153
42DAP/reference	2.254	0.007
43DAP/reference	2.40979	0.007
47DAP/reference	1.44985	0.525
52DAP/reference	1.83768	0.007
57DAP/reference	3.14782	0.004

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.78026	0.04
17DAP/reference	0.75043	0.012
27DAP/reference	0.76776	0.039
39DAP/reference	0.72616	0.018
41DAP/reference	0.78317	0.035
42DAP/reference	0.80066	0.05
43DAP/reference	0.79591	0.144
47DAP/reference	0.88963	0.087
52DAP/reference	0.86548	0.008
57DAP/reference	0.77523	0.037

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	2.03729	0.027
17DAP/reference	1.78863	0.326
27DAP/reference	3.9344	0.02
39DAP/reference	3.26843	0.018
41DAP/reference	2.54472	0.011
42DAP/reference	2.79414	0.019
43DAP/reference	2.4817	0.296
47DAP/reference	1.02935	1
52DAP/reference	2.17662	0.216
57DAP/reference	1.48111	0.827

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.91059	1
26DAP/20DAP	2.14733	0.195
34DAP/26DAP	1.87799	1
51DAP/34DAP	1.00975	0.927
52DAP/51DAP	2.02878	0.035
53DAP/52DAP	1.07385	0.845
55DAP/53DAP	1.19054	0.33
57DAP/55DAP	0.60615	0.057
62DAP/57DAP	0.92747	0.681
68DAP/62DAP	1.43499	0.375
68DAP/14DAP	1.27218	0.615

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.56959	0.037

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.82148
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	1.1101	1
Mature Eggplant/Ripe Tomato	1.21864

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	1.2035	0.694
1-3/M82	N/A	N/A
2-1-1/M82	0.77574
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	1.10866
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	N/A	N/A
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	N/A	N/A
WT/WTpooled	0.74709

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	0.83698	0.497

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.14733	0.921
DC3000/delta hrp 6h	0.40558
DC3000/delta hrp 12h	1.00871	1
DC3000/delta hrp 24h	1.23759	0.271

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.11451	0.441
DC3000 delta B/DC3000 delta AB	1.10468	0.479

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.83939	1
Exp 36h	N/A	N/A
Exp 60h	1.05637	1

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

hybridization	ratio	FDR (corrected p value)
self-self	0.98236	1
Var 0h	N/A	N/A
Var 12h I row2-row1	1.17378	0.324
Var 12h NI row2-row1	1.19827	0.34
Var 36h I row2-row1	0.89494
Var 36h NI row2-row1	1.08761	1
Var 60h I row2-row1	0.78135	0.439
Var 60h NI row2-row1	0.77172	1
Time course 0hI-0hNI	0.85026	0.071
Time course 12hI-12hNI	0.97118	0.847
Time course 36hI-36hNI	0.84421	0.134
Time course 60hI-60hNI	0.65783	0.026

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)	1.16812	0.273
transgenic ySAMdc/azygous control (breaker)	0.84736	0.173
transgenic ySAMdc/azygous control (red)	0.92335	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.01641	0.471

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.10223	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.00234	1
Manapal/WT (break)	1.03687	1
Manapal/WT (red)	0.86571	0.36