Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.1.17.18

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.08222	0.786
27DAP/17DAP	1.02531	1
39DAP/27DAP	1.55743	0.057
41DAP/39DAP	0.7328	0.148
42DAP/41DAP	1.45764	0.856
43DAP/42DAP	1.11087	1
47DAP/43DAP	0.93773	0.754
52DAP/47DAP	1.1894	0.715
57DAP/52DAP	1.37475	0.837

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.00092	0.771
17DAP/reference	1.13979	0.138
27DAP/reference	1.09468	0.365
39DAP/reference	1.27523	0.015
41DAP/reference	1.17625	0.015
42DAP/reference	1.46841	0.001
43DAP/reference	1.2735	0.026
47DAP/reference	1.54793	0.001
52DAP/reference	1.29265	0.015
57DAP/reference	1.27954	0.01

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.03695	0.762
27DAP/17DAP	1.11858	0.699
39DAP/27DAP	0.86413	0.156
41DAP/39DAP	1.01775	1
42DAP/41DAP	1.09476	0.571
43DAP/42DAP	1.02423	1
47DAP/43DAP	1.00055	1
52DAP/47DAP	0.9067	0.472
57DAP/52DAP	1.16432	0.368
57DAP/7DAP	0.65817	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.95585	0.326
17DAP/reference	0.9581	0.044
27DAP/reference	0.98854	0.462
39DAP/reference	0.95062	0.17
41DAP/reference	0.94348	0.133
42DAP/reference	0.90299	0.014
43DAP/reference	0.96488	0.183
47DAP/reference	1.07845	0.561
52DAP/reference	0.92583	0.126
57DAP/reference	0.91806	0.052

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.04932	0.776
17DAP/reference	1.15779	0.223
27DAP/reference	1.45553	0.017
39DAP/reference	1.18313	0.106
41DAP/reference	1.2124	0.07
42DAP/reference	1.15932	0.359
43DAP/reference	1.03091	0.997
47DAP/reference	1.21602	0.045
52DAP/reference	1.0924	0.471
57DAP/reference	1.10795	0.567

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.9746	0.422
17DAP/reference	0.97262	0.579
27DAP/reference	1.00016	1
39DAP/reference	0.97767	0.299
41DAP/reference	0.96395	0.293
42DAP/reference	1.1848	0.258
43DAP/reference	1.22642	0.214
47DAP/reference	1.22207	0.085
52DAP/reference	1.22778	0.176
57DAP/reference	1.57071	0.036

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.31257	0.966
26DAP/20DAP	1.59488	0.118
34DAP/26DAP	1.0545	1
51DAP/34DAP	1.13441	0.627
52DAP/51DAP	0.9842	1
53DAP/52DAP	1.13372	0.187
55DAP/53DAP	1.09664	0.275
57DAP/55DAP	1.18894	0.61
62DAP/57DAP	0.63758	0.016
68DAP/62DAP	1.22529	0.747
68DAP/14DAP	1.05941	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.56215	0.022

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.88327	0.384
Mature Green Tomato/Ripe Tomato	0.77064	0.148
Immature Eggplant/Mature Eggplant	0.91661	0.366
Ripe Pepper/Ripe Tomato	0.98197	1
Mature Eggplant/Ripe Tomato	0.67829	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.95438	0.944
1-1-2/M82	1.23189	1
12-2/M82	0.97863	1
12-4/M82	0.9761	1
1-3/M82	1.84446	0.479
2-1-1/M82	1.17896
2-1/M82	1.30811
2-6/M82	0.7635	1
3-2/M82	1.32676
4-1-1/M82	1.03078	1
4-1/M82	1.31189	1
4-3-2/M82	1.02893	1
4-3/M82	1.33729	1
5-3/M82	0.95107	1
6-2/M82	N/A	N/A
6-3/M82	0.69309	1
7-1/M82	1.0372	0.598
7-2/M82	1.09135
9-3-2/M82	1.41957	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	0.45785
IL7-3/WTpooled	1.0608
IL12-4/WTpooled	N/A	N/A
IL1-4/WTpooled	1.09299
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	1.01799	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.01977	1
DC3000/delta hrp 6h	1.13169	0.857
DC3000/delta hrp 12h	1.11826	1
DC3000/delta hrp 24h	0.82036	0.049

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.24539	0.049
DC3000 delta B/DC3000 delta AB	1.37372	0.09

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.27461	1
Exp 36h	0.90441	0.699
Exp 60h	1.00456	1

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

hybridization	ratio	FDR (corrected p value)
self-self	1.0051	1
Var 0h	0.91977	1
Var 12h I row2-row1	0.97047	0.856
Var 12h NI row2-row1	1.09499	1
Var 36h I row2-row1	1.26326	0.298
Var 36h NI row2-row1	1.06631	1
Var 60h I row2-row1	0.80071	0.374
Var 60h NI row2-row1	0.91639	0.977
Time course 0hI-0hNI	1.11019	0.486
Time course 12hI-12hNI	0.99033	0.972
Time course 36hI-36hNI	1.14672	0.089
Time course 60hI-60hNI	1.47162	0.013

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)	1.0039	1
transgenic ySAMdc/azygous control (breaker)	0.79194	0.131
transgenic ySAMdc/azygous control (red)	0.89869	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.08378	0.448

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.74923	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.96289	1
Manapal/WT (break)	0.91256	1
Manapal/WT (red)	0.90623	0.503