Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.4.13.19

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.97631	0.752
27DAP/17DAP	1.67399	0.677
39DAP/27DAP	0.9749	0.769
41DAP/39DAP	1.08236	0.293
42DAP/41DAP	1.146	0.868
43DAP/42DAP	1.09114	1
47DAP/43DAP	1.22167	0.415
52DAP/47DAP	0.99615	0.957
57DAP/52DAP	1.08738	0.983

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.04155	0.872
17DAP/reference	1.18451	0.015
27DAP/reference	1.11138	0.051
39DAP/reference	1.06805	0.089
41DAP/reference	1.21479	0.021
42DAP/reference	0.89459	0.017
43DAP/reference	1.04804	0.596
47DAP/reference	0.8945	0.038
52DAP/reference	0.83148	0.04
57DAP/reference	0.8576	0.118

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.16885	0.438
27DAP/17DAP	1.07059	0.747
39DAP/27DAP	0.99388	0.984
41DAP/39DAP	1.06014	0.868
42DAP/41DAP	0.93936	0.607
43DAP/42DAP	1.09917	0.273
47DAP/43DAP	1.03675	0.969
52DAP/47DAP	1.02093	0.987
57DAP/52DAP	1.04063	0.763
57DAP/7DAP	1.07327	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.12202	0.263
17DAP/reference	1.17265	0.018
27DAP/reference	0.9489	0.264
39DAP/reference	1.12667	0.038
41DAP/reference	1.1657	0.043
42DAP/reference	1.11743	0.308
43DAP/reference	1.11384	0.105
47DAP/reference	1.11715	0.618
52DAP/reference	0.9684	0.278
57DAP/reference	1.14615	0.082

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.06112	0.524
17DAP/reference	0.99697	0.747
27DAP/reference	0.90119	0.144
39DAP/reference	0.94119	0.298
41DAP/reference	0.8365	0.091
42DAP/reference	0.83297	0.032
43DAP/reference	0.9793	0.561
47DAP/reference	0.91015	0.049
52DAP/reference	0.97297	0.407
57DAP/reference	1.09519	0.286

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.01546	0.804
17DAP/reference	1.03066	0.792
27DAP/reference	0.83189	0.031
39DAP/reference	0.97574	0.544
41DAP/reference	0.89316	0.096
42DAP/reference	0.80594	0.059
43DAP/reference	0.90796	0.305
47DAP/reference	1.02137	1
52DAP/reference	0.86925	0.25
57DAP/reference	0.57963	0.016

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.07949	0.966
26DAP/20DAP	0.96254	1
34DAP/26DAP	1.13064	0.819
51DAP/34DAP	1.44713	0.402
52DAP/51DAP	1.13816	0.792
53DAP/52DAP	1.0531	0.882
55DAP/53DAP	1.06854	0.537
57DAP/55DAP	0.9368	0.736
62DAP/57DAP	1.05768	0.833
68DAP/62DAP	0.81234	0.429
68DAP/14DAP	0.75963	0.121

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.82859	0.358

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.9244
Mature Green Tomato/Ripe Tomato	N/A	N/A
Immature Eggplant/Mature Eggplant	0.50574	0.081
Ripe Pepper/Ripe Tomato	0.92161	1
Mature Eggplant/Ripe Tomato	0.33872

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.08702	0.877
1-1-2/M82	1.04225	1
12-2/M82	1.00922	1
12-4/M82	0.95177
1-3/M82	1.59431
2-1-1/M82	0.7778	0.465
2-1/M82	0.57018
2-6/M82	1.43136	0.374
3-2/M82	1.72613
4-1-1/M82	1.27672	1
4-1/M82	N/A	N/A
4-3-2/M82	N/A	N/A
4-3/M82	1.25648	1
5-3/M82	0.78441	0.49
6-2/M82	1.63618	1
6-3/M82	1.23656	1
7-1/M82	1.09935
7-2/M82	1.23677
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.95309	0.321
IL2-6/WTpooled	0.99495	1
IL7-5/WTpooled	1.00831	1
IL7-3/WTpooled	0.81539	0.418
IL12-4/WTpooled	0.99791	1
IL1-4/WTpooled	0.89955	0.834
WT/WTpooled	1.05625	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	0.84402

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.04362	0.914
DC3000/delta hrp 6h	0.48427	0.637
DC3000/delta hrp 12h	1.17501	1
DC3000/delta hrp 24h	1.50728	0.025

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	0.96865	1
Exp 36h	0.98482	1
Exp 60h	0.87254	0.754

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

hybridization	ratio	FDR (corrected p value)
self-self	1.04847	1
Var 0h	2.3781	1
Var 12h I row2-row1	1.28443	0.544
Var 12h NI row2-row1	0.541	1
Var 36h I row2-row1	0.96101
Var 36h NI row2-row1	0.39251	1
Var 60h I row2-row1	1.14835
Var 60h NI row2-row1	0.78323	0.63
Time course 0hI-0hNI	1.11549	0.852
Time course 12hI-12hNI	1.02552	0.972
Time course 36hI-36hNI	1.12347	0.799
Time course 60hI-60hNI	5.52268	0.216

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)	1.11021	0.294
transgenic ySAMdc/azygous control (breaker)	1.31198	0.178
transgenic ySAMdc/azygous control (red)	1.05666	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.97002	0.22

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.27992	0.239

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	3.59727	0.083
Manapal/WT (break)	3.44928	0.13
Manapal/WT (red)	1.5031	1