Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.1.1.18

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.03744	0.932
27DAP/17DAP	1.1576	0.845
39DAP/27DAP	1.05703	0.946
41DAP/39DAP	1.11816	0.814
42DAP/41DAP	0.94406	1
43DAP/42DAP	0.95992	0.887
47DAP/43DAP	1.0047	0.913
52DAP/47DAP	1.27428	0.556
57DAP/52DAP	1.09216	0.849

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.0106	1
17DAP/reference	0.92727	0.053
27DAP/reference	1.0015	1
39DAP/reference	0.96109	0.315
41DAP/reference	0.91777	0.542
42DAP/reference	1.082	0.241
43DAP/reference	0.99268	0.805
47DAP/reference	1.07311	0.085
52DAP/reference	1.25891	0.092
57DAP/reference	1.12643	0.141

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.0469	0.569
27DAP/17DAP	1.02473	0.924
39DAP/27DAP	0.96825	0.628
41DAP/39DAP	1.03689	0.753
42DAP/41DAP	1.02432	0.872
43DAP/42DAP	0.99873	1
47DAP/43DAP	0.95511	0.499
52DAP/47DAP	1.04108	0.868
57DAP/52DAP	0.96612	0.501
57DAP/7DAP	0.99184	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.04294	0.511
17DAP/reference	1.09283	0.015
27DAP/reference	1.07619	0.013
39DAP/reference	1.00208	1
41DAP/reference	1.08867	0.121
42DAP/reference	0.98824	0.482
43DAP/reference	1.00426	1
47DAP/reference	0.9771	0.504
52DAP/reference	1.07387	0.308
57DAP/reference	1.02701	0.356

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.05702	0.294
17DAP/reference	1.04147	0.628
27DAP/reference	1.10356	0.174
39DAP/reference	1.26434	0.026
41DAP/reference	1.12274	0.459
42DAP/reference	1.06287	0.621
43DAP/reference	1.05467	0.411
47DAP/reference	1.09916	0.045
52DAP/reference	0.93253	0.433
57DAP/reference	1.13047	0.08

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.05441	0.481
17DAP/reference	0.98782	0.668
27DAP/reference	1.0041	1
39DAP/reference	1.02724	0.365
41DAP/reference	1.0317	0.397
42DAP/reference	1.10964	0.127
43DAP/reference	1.12834	0.139
47DAP/reference	0.99157	0.626
52DAP/reference	1.05924	0.517
57DAP/reference	1.20129	0.157

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.99969	1
26DAP/20DAP	1.03201	0.962
34DAP/26DAP	1.04432	1
51DAP/34DAP	1.10697	0.627
52DAP/51DAP	1.04123	0.776
53DAP/52DAP	N/A	N/A
55DAP/53DAP	1.19368	0.653
57DAP/55DAP	0.91191	0.587
62DAP/57DAP	0.79335
68DAP/62DAP	1.1968	0.515
68DAP/14DAP	1.03906	0.85

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.02575	0.908

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.21239
Mature Green Tomato/Ripe Tomato	0.83891	0.317
Immature Eggplant/Mature Eggplant	1.25754	0.321
Ripe Pepper/Ripe Tomato	1.31093	1
Mature Eggplant/Ripe Tomato	1.72431	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.89645	0.934
1-1-2/M82	1.00435	1
12-2/M82	0.89143	0.955
12-4/M82	0.93614	0.358
1-3/M82	0.94028	1
2-1-1/M82	1.07781	1
2-1/M82	1.32996	1
2-6/M82	0.95493	1
3-2/M82	1.06006	0.717
4-1-1/M82	0.91395	1
4-1/M82	0.8861	0.737
4-3-2/M82	0.81709	0.487
4-3/M82	0.95764	1
5-3/M82	0.95569	1
6-2/M82	1.00096	1
6-3/M82	1.0454	1
7-1/M82	1.01168	1
7-2/M82	0.99868	1
9-3-2/M82	0.86617	0.355

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.99691	1
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	0.93495	1
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	N/A	N/A
IL1-4/WTpooled	0.98447	1
WT/WTpooled	N/A	N/A

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	0.93577	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.89787	0.941
DC3000/delta hrp 6h	1.67006	1
DC3000/delta hrp 12h	1.06801	1
DC3000/delta hrp 24h	1.0951	0.383

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.06431	0.408
DC3000 delta B/DC3000 delta AB	1.02959	0.593

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.01587	1
Exp 36h	N/A	N/A
Exp 60h	0.86822	0.586

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

hybridization	ratio	FDR (corrected p value)
self-self	1.0019	1
Var 0h	1.04829	0.98
Var 12h I row2-row1	1.06454	0.348
Var 12h NI row2-row1	1.05186	1
Var 36h I row2-row1	1.01201	1
Var 36h NI row2-row1	1.06746	1
Var 60h I row2-row1	1.35312	1
Var 60h NI row2-row1	1.1169	0.904
Time course 0hI-0hNI	1.14368	0.764
Time course 12hI-12hNI	1.05873	0.754
Time course 36hI-36hNI	0.91346	0.19
Time course 60hI-60hNI	1.0463	0.575

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)	0.97268	0.722
transgenic ySAMdc/azygous control (breaker)	1.10128	1
transgenic ySAMdc/azygous control (red)	1.19299	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.95113	0.062

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.31866	0.239

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.04532	0.307
Manapal/WT (break)	1.38665	0.183
Manapal/WT (red)	1.29745	0.164