Tomato Functional Genomics Database (TFGD)

Expression of 1-1-8.1.1.4

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.14632	0.63
27DAP/17DAP	1.14127	1
39DAP/27DAP	3.21489	0.025
41DAP/39DAP	1.1058	0.921
42DAP/41DAP	0.66127	0.397
43DAP/42DAP	0.88783	0.694
47DAP/43DAP	0.56584	0.067
52DAP/47DAP	1.58093	0.251
57DAP/52DAP	0.93356	0.926

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.1935	0.071
17DAP/reference	1.21837	0.039
27DAP/reference	1.15442	0.2
39DAP/reference	1.15492	0.249
41DAP/reference	1.16878	0.015
42DAP/reference	1.21008	0.007
43DAP/reference	1.01518	0.957
47DAP/reference	1.25859	0.002
52DAP/reference	1.43508	0.008
57DAP/reference	1.22477	0.088

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.25423	0.051
27DAP/17DAP	1.11021	0.65
39DAP/27DAP	1.16333	0.46
41DAP/39DAP	1.39634	0.407
42DAP/41DAP	0.8968	0.284
43DAP/42DAP	0.90512	0.206
47DAP/43DAP	1.01057	0.973
52DAP/47DAP	0.82166	0.22
57DAP/52DAP	1.01088	0.913
57DAP/7DAP	0.69069	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.86673	0.146
17DAP/reference	0.7731	0.012
27DAP/reference	0.68461	0.01
39DAP/reference	0.77174	0.011
41DAP/reference	0.84757	0.029
42DAP/reference	0.73492	0.01
43DAP/reference	0.71412	0.016
47DAP/reference	0.93031	0.504
52DAP/reference	0.68234	0.016
57DAP/reference	0.78572	0.012

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.13881	0.424
17DAP/reference	1.2469	0.131
27DAP/reference	1.1927	0.06
39DAP/reference	1.46869	0.036
41DAP/reference	1.33593	0.016
42DAP/reference	1.25205	0.028
43DAP/reference	1.20462	0.239
47DAP/reference	1.02478	1
52DAP/reference	1.46117	0.012
57DAP/reference	1.45745	0.007

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.78817	0.063
17DAP/reference	0.99226	0.763
27DAP/reference	0.6858	0.024
39DAP/reference	0.70433	0.02
41DAP/reference	0.81383	0.064
42DAP/reference	0.83966	0.22
43DAP/reference	0.99884	0.568
47DAP/reference	1.14121	0.228
52DAP/reference	0.67239	0.079
57DAP/reference	1.1246	0.436

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.1213	1
26DAP/20DAP	1.46791	0.106
34DAP/26DAP	1.17952	0.089
51DAP/34DAP	1.20787	0.303
52DAP/51DAP	0.83425	1
53DAP/52DAP	1.02155	0.944
55DAP/53DAP	1.0881	0.782
57DAP/55DAP	1.09523	0.854
62DAP/57DAP	0.6596	0.871
68DAP/62DAP	0.66972	0.609
68DAP/14DAP	0.94728	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.69658	0.015

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.96287	0.058
Mature Green Tomato/Ripe Tomato	1.05473	1
Immature Eggplant/Mature Eggplant	0.72582	0.071
Ripe Pepper/Ripe Tomato	0.65142	1
Mature Eggplant/Ripe Tomato	0.93654	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	0.63482
12-2/M82	N/A	N/A
12-4/M82	1.05615	1
1-3/M82	2.44447
2-1-1/M82	0.60403
2-1/M82	N/A	N/A
2-6/M82	N/A	N/A
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	1.01414
5-3/M82	2.74761	0.378
6-2/M82	3.05865
6-3/M82	N/A	N/A
7-1/M82	1.62735
7-2/M82	1.06936	1
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.92853	0.321
IL2-6/WTpooled	0.94885	1
IL7-5/WTpooled	1.2834	1
IL7-3/WTpooled	0.99646	1
IL12-4/WTpooled	0.9466	1
IL1-4/WTpooled	0.95168	1
WT/WTpooled	0.94345	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	1.09034	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.10665	0.921
DC3000/delta hrp 6h	0.87957	0.95
DC3000/delta hrp 12h	1.25376	1
DC3000/delta hrp 24h	0.93385	0.575

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.91841	0.724
DC3000 delta B/DC3000 delta AB	1.13209	0.341

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.99031	1
Exp 36h	1.02248	1
Exp 60h	0.89867	0.343

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

hybridization	ratio	FDR (corrected p value)
self-self	0.98631	1
Var 0h	0.34443	1
Var 12h I row2-row1	1.00287	1
Var 12h NI row2-row1	1.0669	0.649
Var 36h I row2-row1	1.15678	0.601
Var 36h NI row2-row1	0.75494	0.549
Var 60h I row2-row1	0.9088	0.952
Var 60h NI row2-row1	0.85477	0.818
Time course 0hI-0hNI	1.06227	0.662
Time course 12hI-12hNI	1.17472	0.287
Time course 36hI-36hNI	1.45488	0.006
Time course 60hI-60hNI	3.66584	0.008

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)	0.99386	0.931
transgenic ySAMdc/azygous control (breaker)	0.79659	0.251
transgenic ySAMdc/azygous control (red)	1.10929	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.90811	0.133

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.18188	0.229

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.11166	1
Manapal/WT (break)	1.70885	0.183
Manapal/WT (red)	0.58204	0.503