Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.4.11.6

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.12617	0.786
27DAP/17DAP	1.22837	0.769
39DAP/27DAP	1.01797	0.857
41DAP/39DAP	1.05886	0.758
42DAP/41DAP	1.39999	0.507
43DAP/42DAP	0.95492	0.895
47DAP/43DAP	1.21581	0.569
52DAP/47DAP	0.95498	0.837
57DAP/52DAP	0.81391	0.622

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.9146	0.194
17DAP/reference	1.04129	0.565
27DAP/reference	0.88594	0.147
39DAP/reference	0.95023	0.527
41DAP/reference	1.00555	1
42DAP/reference	1.1388	0.151
43DAP/reference	0.94913	0.48
47DAP/reference	0.98309	0.473
52DAP/reference	0.81556	0.035
57DAP/reference	0.95142	0.235

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.14688	0.196
27DAP/17DAP	0.93944	0.854
39DAP/27DAP	1.20696	0.3
41DAP/39DAP	1.05257	0.849
42DAP/41DAP	1.06522	0.999
43DAP/42DAP	1.02229	0.699
47DAP/43DAP	1.06474	0.681
52DAP/47DAP	1.09235	0.639
57DAP/52DAP	0.94872	0.558
57DAP/7DAP	1.39725	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.95759	0.402
17DAP/reference	0.88567	0.094
27DAP/reference	0.94355	0.248
39DAP/reference	0.81703	0.049
41DAP/reference	0.81212	0.027
42DAP/reference	0.87029	0.1
43DAP/reference	1.03965	0.537
47DAP/reference	0.84455	0.293
52DAP/reference	0.81187	0.012
57DAP/reference	1.07544	0.799

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.09187	0.538
17DAP/reference	0.87203	0.149
27DAP/reference	0.85623	0.129
39DAP/reference	0.8403	0.087
41DAP/reference	0.96795	0.441
42DAP/reference	0.86961	0.098
43DAP/reference	1.12613	0.485
47DAP/reference	1.06717	0.675
52DAP/reference	0.87909	0.101
57DAP/reference	1.09033	0.523

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.99575	0.75
17DAP/reference	0.94082	0.426
27DAP/reference	1.01221	0.903
39DAP/reference	1.07236	0.146
41DAP/reference	1.07581	0.471
42DAP/reference	0.93544	0.445
43DAP/reference	0.91247	0.334
47DAP/reference	0.92842	0.286
52DAP/reference	1.05356	0.928
57DAP/reference	1.02968	0.878

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.93716	1
26DAP/20DAP	1.00601	1
34DAP/26DAP	1.22982	0.542
51DAP/34DAP	1.13891	0.473
52DAP/51DAP	0.97585	1
53DAP/52DAP	1.06119	0.921
55DAP/53DAP	1.03723	0.955
57DAP/55DAP	0.93891	0.684
62DAP/57DAP	0.89032	0.681
68DAP/62DAP	1.01348	0.885
68DAP/14DAP	1.50532	0.17

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.30332	0.663

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	1.1558	0.881
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	1.49401	0.258
Mature Eggplant/Ripe Tomato	1.01267	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	0.74255
12-2/M82	N/A	N/A
12-4/M82	0.88719	1
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	0.89978
4-1-1/M82	N/A	N/A
4-1/M82	0.8647
4-3-2/M82	0.90219
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	0.97036	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.77624	0.243
IL2-6/WTpooled	1.19036	0.659
IL7-5/WTpooled	1.2928	1
IL7-3/WTpooled	0.64339	0.298
IL12-4/WTpooled	0.99136	1
IL1-4/WTpooled	1.25013	1
WT/WTpooled	1.03629	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	1.21196	0.479

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.18447	0.758
DC3000/delta hrp 6h	0.89717	0.95
DC3000/delta hrp 12h	0.95488	1
DC3000/delta hrp 24h	1.25332	0.728

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	2.15144	0.326
Exp 60h	0.91501	0.586

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

hybridization	ratio	FDR (corrected p value)
self-self	1.01047	1
Var 0h	N/A	N/A
Var 12h I row2-row1	1.0347	0.544
Var 12h NI row2-row1	1.01782	1
Var 36h I row2-row1	1.14807	0.908
Var 36h NI row2-row1	1.27214	1
Var 60h I row2-row1	1.12552	1
Var 60h NI row2-row1	0.96401	1
Time course 0hI-0hNI	1.06143	0.719
Time course 12hI-12hNI	1.0167	0.786
Time course 36hI-36hNI	1.29551	0.009
Time course 60hI-60hNI	1.81257	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)	0.98039	0.454
transgenic ySAMdc/azygous control (breaker)	1.38883	0.162
transgenic ySAMdc/azygous control (red)	0.98419	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.03279	0.273

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.93321	0.431

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.77177	1
Manapal/WT (break)	0.92618	1
Manapal/WT (red)	0.8407	0.36