Tomato Functional Genomics Database (TFGD)

Expression of 1-1-8.4.3.17

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.04658	0.997
27DAP/17DAP	1.55263	0.633
39DAP/27DAP	0.8324	0.326
41DAP/39DAP	0.98275	0.857
42DAP/41DAP	0.84897	0.774
43DAP/42DAP	0.90718	0.846
47DAP/43DAP	1.36133	0.49
52DAP/47DAP	1.34166	0.652
57DAP/52DAP	1.10382	0.935

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.88885	0.246
17DAP/reference	0.90778	0.503
27DAP/reference	1.00606	1
39DAP/reference	0.98988	0.874
41DAP/reference	1.10493	0.393
42DAP/reference	0.77996	0.016
43DAP/reference	0.80575	0.631
47DAP/reference	1.15435	0.989
52DAP/reference	1.10467	0.079
57DAP/reference	N/A	N/A

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.84909	0.245
27DAP/17DAP	0.97461	0.887
39DAP/27DAP	1.10016	0.532
41DAP/39DAP	1.01479	1
42DAP/41DAP	0.96308	0.679
43DAP/42DAP	0.94341	0.684
47DAP/43DAP	0.98814	0.93
52DAP/47DAP	0.82795	0.446
57DAP/52DAP	1.45011	0.584
57DAP/7DAP	1.60539	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.20982	0.11
17DAP/reference	1.51207	0.009
27DAP/reference	1.29068	0.107
39DAP/reference	1.39109	0.007
41DAP/reference	1.27978	0.043
42DAP/reference	1.63877	0.006
43DAP/reference	1.46666	0.014
47DAP/reference	1.26502	0.169
52DAP/reference	1.374	0.012
57DAP/reference	1.49543	0.008

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.10888	0.3
17DAP/reference	1.03704	0.999
27DAP/reference	1.11583	0.212
39DAP/reference	1.06119	1
41DAP/reference	1.04387	1
42DAP/reference	1.20581	0.153
43DAP/reference	1.20631	0.396
47DAP/reference	0.91226	0.188
52DAP/reference	1.2403	0.007
57DAP/reference	0.91992	0.361

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.19042	0.212
17DAP/reference	1.32143	0.298
27DAP/reference	1.50312	0.023
39DAP/reference	1.6139	0.005
41DAP/reference	1.51457	0.009
42DAP/reference	1.3355	0.029
43DAP/reference	1.32685	0.121
47DAP/reference	0.99089	0.626
52DAP/reference	1.21945	0.349
57DAP/reference	1.52841	0.017

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.9232	1
26DAP/20DAP	0.82824	0.317
34DAP/26DAP	N/A	N/A
51DAP/34DAP	0.89883	0.667
52DAP/51DAP	0.88066
53DAP/52DAP	0.64119	0.079
55DAP/53DAP	0.95483	0.761
57DAP/55DAP	0.8671	0.577
62DAP/57DAP	1.08371	0.868
68DAP/62DAP	1.80667	0.392
68DAP/14DAP	1.53224	0.035

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.5519	0.415

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.67742	0.249
Mature Green Tomato/Ripe Tomato	1.57022	0.185
Immature Eggplant/Mature Eggplant	1.04682	0.288
Ripe Pepper/Ripe Tomato	2.16646
Mature Eggplant/Ripe Tomato	N/A	N/A

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.0697	1
1-1-2/M82	1.21021
12-2/M82	1.1153	1
12-4/M82	1.02419	1
1-3/M82	1.12698	1
2-1-1/M82	0.80494	0.784
2-1/M82	N/A	N/A
2-6/M82	0.89485	1
3-2/M82	0.92572	1
4-1-1/M82	0.91313	1
4-1/M82	1.96736
4-3-2/M82	0.72983
4-3/M82	0.9631
5-3/M82	0.93789	1
6-2/M82	0.72127	1
6-3/M82	1.11912	1
7-1/M82	0.99628	1
7-2/M82	0.5856	0.578
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	1.05825	0.659
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.31801	1
IL12-4/WTpooled	0.91463	0.71
IL1-4/WTpooled	0.98961
WT/WTpooled	1.00513	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	0.97204	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.20311	0.644
DC3000/delta hrp 6h	0.90935	0.95
DC3000/delta hrp 12h	0.95019	1
DC3000/delta hrp 24h	0.95283	0.7

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	0.95414	1
Exp 36h	0.88597	0.82
Exp 60h	1.44272	0.399

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

hybridization	ratio	FDR (corrected p value)
self-self	N/A	N/A
Var 0h	1.08333
Var 12h I row2-row1	1.13141	0.506
Var 12h NI row2-row1	1.04429
Var 36h I row2-row1	1.09949	0.41
Var 36h NI row2-row1	N/A	N/A
Var 60h I row2-row1	N/A	N/A
Var 60h NI row2-row1	N/A	N/A
Time course 0hI-0hNI	0.99237	1
Time course 12hI-12hNI	1.0126	1
Time course 36hI-36hNI	1.04582	0.248
Time course 60hI-60hNI	1.22737	0.16

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)	0.89994	0.277
transgenic ySAMdc/azygous control (breaker)	0.70744	0.131
transgenic ySAMdc/azygous control (red)	0.87422	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.04496	0.17

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.71512	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.88274	1
Manapal/WT (break)	1.02855	1
Manapal/WT (red)	0.8501	0.229