Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.3.6.10

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.98329	0.752
27DAP/17DAP	0.91612	0.822
39DAP/27DAP	1.41454	0.225
41DAP/39DAP	1.09339	0.722
42DAP/41DAP	0.9601	1
43DAP/42DAP	0.98442	0.93
47DAP/43DAP	0.76661	0.29
52DAP/47DAP	1.29611	0.739
57DAP/52DAP	0.93489	0.923

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.14001	0.587
17DAP/reference	1.30525	0.086
27DAP/reference	1.0356	0.909
39DAP/reference	0.99022	0.901
41DAP/reference	1.06056	0.552
42DAP/reference	1.67436	0.009
43DAP/reference	1.11924	0.34
47DAP/reference	1.49636	0.071
52DAP/reference	0.97139	0.475
57DAP/reference	0.93962	0.277

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.97385	0.716
27DAP/17DAP	1.01948	0.976
39DAP/27DAP	0.82966	0.164
41DAP/39DAP	1.15372	0.753
42DAP/41DAP	0.964	0.787
43DAP/42DAP	1.00617	0.96
47DAP/43DAP	0.91359	0.666
52DAP/47DAP	0.99157	0.917
57DAP/52DAP	1.37844	0.124
57DAP/7DAP	1.2035	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.08268	0.6
17DAP/reference	1.22732	0.134
27DAP/reference	1.1332	0.371
39DAP/reference	1.13477	0.601
41DAP/reference	1.17623	0.104
42DAP/reference	1.20747	0.174
43DAP/reference	1.41951	0.013
47DAP/reference	1.28687	0.2
52DAP/reference	1.41461	0.02
57DAP/reference	1.13457	0.438

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.03009	0.767
17DAP/reference	1.51806	0.023
27DAP/reference	1.34021	0.032
39DAP/reference	1.22414	0.059
41DAP/reference	1.23236	0.112
42DAP/reference	1.362	0.089
43DAP/reference	1.15198	0.15
47DAP/reference	1.20411	0.036
52DAP/reference	1.35508	0.038
57DAP/reference	1.38208	0.007

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.03493	0.723
17DAP/reference	1.02997	0.804
27DAP/reference	1.15841	0.061
39DAP/reference	1.17227	0.029
41DAP/reference	1.44471	0.015
42DAP/reference	1.03838	0.818
43DAP/reference	1.17269	0.259
47DAP/reference	1.37915	0.005
52DAP/reference	1.72926	0.179
57DAP/reference	1.48685	0.013

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.91882	1
26DAP/20DAP	0.73741	0.223
34DAP/26DAP	1.15869	1
51DAP/34DAP	0.64534	0.19
52DAP/51DAP	1.02466	1
53DAP/52DAP	1.10459	0.868
55DAP/53DAP	0.9194	0.544
57DAP/55DAP	1.00338	0.855
62DAP/57DAP	0.90811	0.05
68DAP/62DAP	0.82132	0.543
68DAP/14DAP	0.6952	0.086

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.77337	0.081

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	1.96345	0.026
Immature Eggplant/Mature Eggplant	1.24443
Ripe Pepper/Ripe Tomato	1.04536	1
Mature Eggplant/Ripe Tomato	1.03089	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	1.22381	1
12-2/M82	N/A	N/A
12-4/M82	0.92641	0.619
1-3/M82	0.91924
2-1-1/M82	N/A	N/A
2-1/M82	N/A	N/A
2-6/M82	0.77784
3-2/M82	N/A	N/A
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	0.91031	1
6-2/M82	0.85519
6-3/M82	0.88624	0.982
7-1/M82	1.78404
7-2/M82	N/A	N/A
9-3-2/M82	0.89618

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	N/A	N/A
IL7-3/WTpooled	0.76198
IL12-4/WTpooled	0.8359	0.566
IL1-4/WTpooled	0.96394	0.457
WT/WTpooled	0.83738	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	1.15343	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.13058	0.921
DC3000/delta hrp 6h	1.395	1
DC3000/delta hrp 12h	1.05577	1
DC3000/delta hrp 24h	1.25992	0.052

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	0.94672	0.936

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.98996	1
Exp 36h	0.96385	0.879
Exp 60h	1.07675	0.563

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

hybridization	ratio	FDR (corrected p value)
self-self	1.03784	1
Var 0h	1.12969	0.98
Var 12h I row2-row1	1.02109	1
Var 12h NI row2-row1	1.26585	0.235
Var 36h I row2-row1	0.88961	0.805
Var 36h NI row2-row1	0.90509	0.549
Var 60h I row2-row1	0.92299	0.832
Var 60h NI row2-row1	0.73835	0.63
Time course 0hI-0hNI	1.04809	0.603
Time course 12hI-12hNI	0.88681	0.163
Time course 36hI-36hNI	1.01309	0.881
Time course 60hI-60hNI	1.31466	0.011

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)	1.10042	0.318
transgenic ySAMdc/azygous control (breaker)	0.87155	0.173
transgenic ySAMdc/azygous control (red)	1.0073	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.99412	0.673

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.0752	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.90541	1
Manapal/WT (break)	0.93215	1
Manapal/WT (red)	1.267	0.413