Tomato Functional Genomics Database (TFGD)

Expression of 1-1-6.4.17.13

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.14159	0.827
27DAP/17DAP	0.87649	0.777
39DAP/27DAP	1.41459	0.395
41DAP/39DAP	0.9693	0.841
42DAP/41DAP	1.08549	0.978
43DAP/42DAP	0.98241	0.912
47DAP/43DAP	1.40215	0.95
52DAP/47DAP	1.62576	0.818
57DAP/52DAP	0.70442	0.666

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.12459	0.366
17DAP/reference	1.03672	0.717
27DAP/reference	0.98867	0.741
39DAP/reference	0.96778	0.412
41DAP/reference	0.88319	0.114
42DAP/reference	1.03239	0.995
43DAP/reference	0.91824	0.234
47DAP/reference	1.02539	0.773
52DAP/reference	1.09365	0.407
57DAP/reference	1.05973	0.366

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.3104	0.179
27DAP/17DAP	0.91101	0.878
39DAP/27DAP	2.23421	0.611
41DAP/39DAP	0.76712	0.276
42DAP/41DAP	1.04628	1
43DAP/42DAP	1.31246	0.382
47DAP/43DAP	1.20994	0.865
52DAP/47DAP	1.44413	0.374
57DAP/52DAP	0.99339	0.845
57DAP/7DAP	1.12873	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.70678	0.077
17DAP/reference	0.90067	0.22
27DAP/reference	1.13706	0.453
39DAP/reference	0.97969	0.552
41DAP/reference	0.87727	0.203
42DAP/reference	1.08612	1
43DAP/reference	0.85432	0.115
47DAP/reference	0.88955	0.293
52DAP/reference	0.93502	0.304
57DAP/reference	0.83706	0.043

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.99471	0.831
17DAP/reference	1.07336	0.518
27DAP/reference	1.06176	0.704
39DAP/reference	1.26533	0.109
41DAP/reference	1.21638	0.138
42DAP/reference	1.11771	0.38
43DAP/reference	1.02968	0.977
47DAP/reference	1.00771	1
52DAP/reference	1.19846	0.194
57DAP/reference	1.03958	0.957

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.90954	0.119
17DAP/reference	0.9896	0.751
27DAP/reference	1.04309	0.552
39DAP/reference	0.98181	0.643
41DAP/reference	1.58612	0.15
42DAP/reference	1.1758	0.279
43DAP/reference	1.02934	0.88
47DAP/reference	1.07935	0.309
52DAP/reference	1.6457	0.301
57DAP/reference	1.34041	0.035

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.61047	0.966
26DAP/20DAP	0.99802	1
34DAP/26DAP	1.23034	1
51DAP/34DAP	0.70949	0.167
52DAP/51DAP	1.3216	0.439
53DAP/52DAP	0.8566	0.465
55DAP/53DAP	1.32202	0.22
57DAP/55DAP	0.99419	0.867
62DAP/57DAP	1.08539	0.767
68DAP/62DAP	1.34063	0.573
68DAP/14DAP	1.28021	0.802

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.82859	0.399

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.87427	0.446
Immature Eggplant/Mature Eggplant	1.14861	0.15
Ripe Pepper/Ripe Tomato	0.47525	0.293
Mature Eggplant/Ripe Tomato	0.68612	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	1.09368	1
12-2/M82	0.80072
12-4/M82	1.00167	1
1-3/M82	N/A	N/A
2-1-1/M82	0.7189
2-1/M82	N/A	N/A
2-6/M82	N/A	N/A
3-2/M82	1.16138	0.84
4-1-1/M82	N/A	N/A
4-1/M82	N/A	N/A
4-3-2/M82	N/A	N/A
4-3/M82	0.96775	1
5-3/M82	0.80853	1
6-2/M82	1.0982
6-3/M82	N/A	N/A
7-1/M82	1.06358	1
7-2/M82	0.67675
9-3-2/M82	1.05282	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.8088
IL2-6/WTpooled	0.82306	1
IL7-5/WTpooled	0.65998
IL7-3/WTpooled	0.88528	1
IL12-4/WTpooled	0.9126	0.71
IL1-4/WTpooled	0.99112
WT/WTpooled	0.9836	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	1.51494

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.97688	1
DC3000/delta hrp 6h	N/A	N/A
DC3000/delta hrp 12h	1.05786	1
DC3000/delta hrp 24h	0.93678	0.585

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	0.98063	1
Exp 36h	N/A	N/A
Exp 60h	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
self-self	0.84642	1
Var 0h	0.93966	1
Var 12h I row2-row1	0.98786	1
Var 12h NI row2-row1	0.7888	0.82
Var 36h I row2-row1	1.46858	0.908
Var 36h NI row2-row1	1.03251
Var 60h I row2-row1	1.06629	1
Var 60h NI row2-row1	0.91697	0.977
Time course 0hI-0hNI	1.02006	0.852
Time course 12hI-12hNI	1.9344	0.517
Time course 36hI-36hNI	0.93861	0.403
Time course 60hI-60hNI	1.01518	1

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)	0.97183	0.722
transgenic ySAMdc/azygous control (breaker)	0.90212	0.49
transgenic ySAMdc/azygous control (red)	0.96717	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.87141	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.98089	1
Manapal/WT (break)	1.4981	0.183
Manapal/WT (red)	1.81134	0.133