Tomato Functional Genomics Database (TFGD)

Expression of 1-1-5.3.4.20

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.25777	0.77
27DAP/17DAP	0.75173	0.344
39DAP/27DAP	0.75337	0.449
41DAP/39DAP	1.05231	0.844
42DAP/41DAP	1.57861	0.642
43DAP/42DAP	1.36822	0.835
47DAP/43DAP	0.83285	0.462
52DAP/47DAP	1.17777	0.965
57DAP/52DAP	1.12141	0.969

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.22427	0.29
17DAP/reference	0.91861	0.536
27DAP/reference	1.16638	0.051
39DAP/reference	1.07924	0.593
41DAP/reference	0.88761	0.542
42DAP/reference	1.07109	0.756
43DAP/reference	0.67354	0.123
47DAP/reference	1.15163	0.11
52DAP/reference	1.06385	0.766
57DAP/reference	0.20383

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.27934	0.196
27DAP/17DAP	0.96519	0.878
39DAP/27DAP	0.78992	0.149
41DAP/39DAP	1.09427	0.623
42DAP/41DAP	1.0012	0.803
43DAP/42DAP	0.96308	0.709
47DAP/43DAP	0.90403	0.457
52DAP/47DAP	1.01473	0.979
57DAP/52DAP	1.11395	0.806
57DAP/7DAP	0.84883	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.34279	0.028
17DAP/reference	1.33821	0.059
27DAP/reference	1.3048	0.013
39DAP/reference	1.30635	0.013
41DAP/reference	1.23005	0.086
42DAP/reference	1.21125	0.016
43DAP/reference	1.10094	0.527
47DAP/reference	1.42593	0.021
52DAP/reference	1.07775	0.352
57DAP/reference	1.10931	0.183

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.94062	0.607
17DAP/reference	0.85961	0.153
27DAP/reference	1.02165	1
39DAP/reference	1.30622	0.164
41DAP/reference	1.47674	0.005
42DAP/reference	1.80598	0.05
43DAP/reference	0.88103	0.092
47DAP/reference	1.27889	0.008
52DAP/reference	1.21193	0.065
57DAP/reference	0.99429	0.581

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.66791	0.016
17DAP/reference	1.18108	0.503
27DAP/reference	1.3638	0.033
39DAP/reference	1.29982	0.016
41DAP/reference	1.17048	0.072
42DAP/reference	1.16722	0.22
43DAP/reference	1.20802	0.114
47DAP/reference	1.19998	0.035
52DAP/reference	1.12623	0.674
57DAP/reference	1.55791	0.012

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.08943	0.966
26DAP/20DAP	0.7551	0.317
34DAP/26DAP	1.01994	1
51DAP/34DAP	0.63637	0.121
52DAP/51DAP	0.79811	1
53DAP/52DAP	1.0715	0.868
55DAP/53DAP	0.83674	0.515
57DAP/55DAP	1.10957	0.666
62DAP/57DAP	1.23784	0.723
68DAP/62DAP	1.61283	0.008
68DAP/14DAP	1.55852	0.024

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.56406	0.02

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.34368
Mature Green Tomato/Ripe Tomato	3.25827	0.026
Immature Eggplant/Mature Eggplant	0.17731
Ripe Pepper/Ripe Tomato	5.04739	0.256
Mature Eggplant/Ripe Tomato	3.51526

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	N/A	N/A
12-2/M82	N/A	N/A
12-4/M82	0.62305
1-3/M82	N/A	N/A
2-1-1/M82	N/A	N/A
2-1/M82	N/A	N/A
2-6/M82	N/A	N/A
3-2/M82	0.70821
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	N/A	N/A
5-3/M82	0.80413
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	1.09422
7-2/M82	N/A	N/A
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.61806	0.243
IL2-6/WTpooled	1.02515	1
IL7-5/WTpooled	0.84722	1
IL7-3/WTpooled	0.87089	1
IL12-4/WTpooled	0.945	0.71
IL1-4/WTpooled	0.91992	1
WT/WTpooled	0.98835	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	0.86115	0.75

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.95809	1
DC3000/delta hrp 6h	1.09727	1
DC3000/delta hrp 12h	1.01483	1
DC3000/delta hrp 24h	0.46812	0.034

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.53019	0.039
DC3000 delta B/DC3000 delta AB	0.34834	0.022

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.92793	1
Exp 36h	0.68981	0.449
Exp 60h	0.6883	0.29

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

hybridization	ratio	FDR (corrected p value)
self-self	0.9927	1
Var 0h	2.21831	0.936
Var 12h I row2-row1	0.81967	0.338
Var 12h NI row2-row1	0.99259	1
Var 36h I row2-row1	1.09369	1
Var 36h NI row2-row1	0.97588	0.791
Var 60h I row2-row1	1.17755
Var 60h NI row2-row1	0.99426	1
Time course 0hI-0hNI	1.07994	0.852
Time course 12hI-12hNI	1.09902	0.621
Time course 36hI-36hNI	1.09211	0.651
Time course 60hI-60hNI	0.30573	0.009

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)	1.15415	0.245
transgenic ySAMdc/azygous control (breaker)	1.43311	0.172
transgenic ySAMdc/azygous control (red)	1.10651	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.03044	0.317

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.62385	0.231

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	4.60624	0.084
Manapal/WT (break)	3.09825	0.14
Manapal/WT (red)	3.47198	0.126