Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.3.19.20

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.84905	0.324
27DAP/17DAP	1.00202	0.994
39DAP/27DAP	1.61126	0.449
41DAP/39DAP	1.58356	0.363
42DAP/41DAP	1.11526	0.994
43DAP/42DAP	0.87871	0.786
47DAP/43DAP	1.02007	0.84
52DAP/47DAP	1.89586	0.205
57DAP/52DAP	0.87593	0.844

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.26582	0.071
17DAP/reference	1.14699	0.086
27DAP/reference	1.02478	0.966
39DAP/reference	1.02869	0.76
41DAP/reference	1.195	0.067
42DAP/reference	1.13661	0.018
43DAP/reference	1.04829	0.403
47DAP/reference	0.99017	0.568
52DAP/reference	0.91428	0.267
57DAP/reference	0.82031	0.013

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.89185	0.211
27DAP/17DAP	1.12398	0.699
39DAP/27DAP	1.0148	0.874
41DAP/39DAP	0.98106	0.997
42DAP/41DAP	0.9032	0.339
43DAP/42DAP	0.93683	0.367
47DAP/43DAP	1.14008	0.281
52DAP/47DAP	0.92918	0.729
57DAP/52DAP	0.96045	0.716
57DAP/7DAP	0.91337	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.94223	0.203
17DAP/reference	0.88645	0.064
27DAP/reference	0.89306	0.045
39DAP/reference	0.95093	0.198
41DAP/reference	0.92978	0.04
42DAP/reference	0.87684	0.063
43DAP/reference	0.73396	0.012
47DAP/reference	0.86141	0.222
52DAP/reference	0.87966	0.028
57DAP/reference	0.83214	0.02

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.14547	0.127
17DAP/reference	1.13492	0.285
27DAP/reference	1.10414	0.249
39DAP/reference	0.91548	0.11
41DAP/reference	0.84127	0.057
42DAP/reference	0.91727	0.15
43DAP/reference	1.19235	0.103
47DAP/reference	0.91847	0.126
52DAP/reference	1.11415	0.092
57DAP/reference	1.2886	0.051

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.98925	0.653
17DAP/reference	0.93431	0.374
27DAP/reference	0.8563	0.055
39DAP/reference	0.88143	0.031
41DAP/reference	1.13296	0.84
42DAP/reference	0.77317	0.018
43DAP/reference	0.89658	0.188
47DAP/reference	0.92673	0.103
52DAP/reference	0.79262	0.128
57DAP/reference	0.59853	0.016

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.12674	1
26DAP/20DAP	0.86465	0.317
34DAP/26DAP	1.25012	0.819
51DAP/34DAP	0.97493	0.844
52DAP/51DAP	1.03898	1
53DAP/52DAP	0.92404	0.649
55DAP/53DAP	1.28008	0.139
57DAP/55DAP	1.29892	0.826
62DAP/57DAP	1.06701	0.935
68DAP/62DAP	0.77535	0.227
68DAP/14DAP	0.45732	0.086

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	2.29552	0.014

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.76942	0.165
Immature Eggplant/Mature Eggplant	1.30097	0.085
Ripe Pepper/Ripe Tomato	0.37836	0.224
Mature Eggplant/Ripe Tomato	0.94915	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.00777	1
1-1-2/M82	1.00026
12-2/M82	1.46164	0.61
12-4/M82	0.88716	0.619
1-3/M82	0.83443	0.339
2-1-1/M82	1.77021	0.457
2-1/M82	N/A	N/A
2-6/M82	1.28993	0.385
3-2/M82	N/A	N/A
4-1-1/M82	1.34718	1
4-1/M82	1.08125	1
4-3-2/M82	1.46336
4-3/M82	1.66225	1
5-3/M82	0.94566	1
6-2/M82	1.10504	1
6-3/M82	0.98069	1
7-1/M82	N/A	N/A
7-2/M82	1.30687	0.385
9-3-2/M82	2.03887	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.93352	0.321
IL2-6/WTpooled	1.57879	0.419
IL7-5/WTpooled	1.28254	0.792
IL7-3/WTpooled	1.20094	1
IL12-4/WTpooled	1.1014	0.532
IL1-4/WTpooled	1.26751	1
WT/WTpooled	1.01871	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	1.06389	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.03911	0.846
DC3000/delta hrp 6h	1.07546	1
DC3000/delta hrp 12h	0.96176	1
DC3000/delta hrp 24h	1.35503	0.031

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.56087	0.044
DC3000 delta B/DC3000 delta AB	1.14765	0.315

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.24162	1
Exp 36h	1.86797	0.489
Exp 60h	2.02146	0.399

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

hybridization	ratio	FDR (corrected p value)
self-self	1.00005	1
Var 0h	0.75798	0.933
Var 12h I row2-row1	1.11241	0.216
Var 12h NI row2-row1	0.81872	0.546
Var 36h I row2-row1	1.20883	0.742
Var 36h NI row2-row1	0.84024	0.469
Var 60h I row2-row1	0.75651	0.439
Var 60h NI row2-row1	1.06329	1
Time course 0hI-0hNI	1.20267	0.451
Time course 12hI-12hNI	1.18038	0.042
Time course 36hI-36hNI	1.94315	0.004
Time course 60hI-60hNI	5.36589	0.008

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)	1.01575	1
transgenic ySAMdc/azygous control (breaker)	0.37058	0.118
transgenic ySAMdc/azygous control (red)	1.08333	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.05866	0.119

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.77053	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.44824	0.086
Manapal/WT (break)	1.07124	1
Manapal/WT (red)	0.31881	0.181