Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.2.19.19

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.7489	0.211
27DAP/17DAP	1.05865	0.902
39DAP/27DAP	0.81039	0.522
41DAP/39DAP	1.08844	0.696
42DAP/41DAP	0.74948	1
43DAP/42DAP	1.53774	0.861
47DAP/43DAP	2.30353	0.702
52DAP/47DAP	1.19821	0.913
57DAP/52DAP	1.65284	1

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.81734	0.025
17DAP/reference	0.78718	0.012
27DAP/reference	0.99198	0.763
39DAP/reference	1.02554	0.786
41DAP/reference	0.83124	0.049
42DAP/reference	0.87617	0.006
43DAP/reference	0.85992	0.018
47DAP/reference	0.99789	0.636
52DAP/reference	1.16568	0.286
57DAP/reference	1.21731	0.03

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.17708	0.593
27DAP/17DAP	0.8719	0.748
39DAP/27DAP	0.97824	0.844
41DAP/39DAP	0.78628	0.764
42DAP/41DAP	1.77561	0.017
43DAP/42DAP	1.04818	0.664
47DAP/43DAP	1.09956	0.956
52DAP/47DAP	1.02504	0.935
57DAP/52DAP	1.04592	0.838
57DAP/7DAP	1.47416

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.90956	0.203
17DAP/reference	0.81717	0.031
27DAP/reference	0.79036	0.011
39DAP/reference	1.38033	0.077
41DAP/reference	1.04922	0.977
42DAP/reference	1.16054	0.405
43DAP/reference	0.74678	0.018
47DAP/reference	1.06541	0.804
52DAP/reference	0.70687	0.016
57DAP/reference	0.74977	0.021

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.89181	0.286
17DAP/reference	0.67703	0.008
27DAP/reference	0.94201	0.366
39DAP/reference	0.86278	0.064
41DAP/reference	0.94898	0.262
42DAP/reference	0.8695	0.055
43DAP/reference	0.994	0.67
47DAP/reference	0.96398	0.284
52DAP/reference	0.96478	0.38
57DAP/reference	0.70167	0.005

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.82265	0.063
17DAP/reference	0.89156	0.328
27DAP/reference	1.00971	0.763
39DAP/reference	1.02801	0.885
41DAP/reference	1.16646	0.129
42DAP/reference	0.98731	0.816
43DAP/reference	1.01089	1
47DAP/reference	0.9041	0.269
52DAP/reference	0.79907	0.158
57DAP/reference	1.06868	0.636

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.0405	0.966
26DAP/20DAP	1.34697	0.275
34DAP/26DAP	1.12808	1
51DAP/34DAP	1.04528	1
52DAP/51DAP	1.346	0.232
53DAP/52DAP	0.87005	0.677
55DAP/53DAP	0.95101	0.735
57DAP/55DAP	0.96085	0.845
62DAP/57DAP	0.69542	0.28
68DAP/62DAP	1.25596	0.713
68DAP/14DAP	2.22185	0.019

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.49932	0.022

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.26745	0.073
Mature Green Tomato/Ripe Tomato	N/A	N/A
Immature Eggplant/Mature Eggplant	1.78029	0.05
Ripe Pepper/Ripe Tomato	4.28861	0.258
Mature Eggplant/Ripe Tomato	1.78268	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.02369	1
1-1-2/M82	1.0835	0.977
12-2/M82	1.15494
12-4/M82	0.8864	0.619
1-3/M82	0.8229
2-1-1/M82	0.73296	0.784
2-1/M82	1.0123	1
2-6/M82	0.72261	1
3-2/M82	N/A	N/A
4-1-1/M82	0.48102
4-1/M82	N/A	N/A
4-3-2/M82	0.6666
4-3/M82	0.78416
5-3/M82	1.04267	1
6-2/M82	0.67472	0.481
6-3/M82	1.10079	1
7-1/M82	N/A	N/A
7-2/M82	0.83036	0.565
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	1.05991	1
IL7-5/WTpooled	1.311	0.792
IL7-3/WTpooled	0.86029	0.418
IL12-4/WTpooled	1.09374	0.737
IL1-4/WTpooled	0.9393	0.834
WT/WTpooled	0.97094	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	1.43156

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.03183	1
DC3000/delta hrp 6h	0.86184	0.95
DC3000/delta hrp 12h	0.93387	1
DC3000/delta hrp 24h	0.85581	0.323

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	1.14842	1
Exp 36h	1.12154	1
Exp 60h	1.34449	0.283

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

hybridization	ratio	FDR (corrected p value)
self-self	0.88518	1
Var 0h	0.99628	1
Var 12h I row2-row1	0.88381	0.318
Var 12h NI row2-row1	0.99876	1
Var 36h I row2-row1	0.84188	0.374
Var 36h NI row2-row1	0.84163	0.791
Var 60h I row2-row1	0.91675	0.582
Var 60h NI row2-row1	0.89529	0.904
Time course 0hI-0hNI	1.0612	0.662
Time course 12hI-12hNI	0.92119	0.522
Time course 36hI-36hNI	0.9428	0.36
Time course 60hI-60hNI	0.76602	0.047

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)	0.86285	0.299
transgenic ySAMdc/azygous control (breaker)	0.85231	0.173
transgenic ySAMdc/azygous control (red)	0.87054	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.28141	0.038

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.9069	0.284

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.04839	1
Manapal/WT (break)	0.86449	1
Manapal/WT (red)	0.93542	0.229