Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.3.17.6

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.96713	0.779
27DAP/17DAP	1.30352	0.735
39DAP/27DAP	1.00209	0.733
41DAP/39DAP	1.84005	0.306
42DAP/41DAP	1.29515	0.994
43DAP/42DAP	1.09838	1
47DAP/43DAP	1.08237	0.769
52DAP/47DAP	0.78938	0.538
57DAP/52DAP	0.85396	0.85

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.83903	0.08
17DAP/reference	0.75644	0.007
27DAP/reference	1.01893	1
39DAP/reference	0.85596	0.106
41DAP/reference	0.71465	0.009
42DAP/reference	0.85664	0.017
43DAP/reference	0.88865	0.088
47DAP/reference	0.95968	0.3
52DAP/reference	1.18413	0.043
57DAP/reference	1.14293	0.04

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.8287	0.044
27DAP/17DAP	1.13894	0.859
39DAP/27DAP	0.73144	0.118
41DAP/39DAP	0.94595	0.959
42DAP/41DAP	1.06903	0.85
43DAP/42DAP	1.04614	0.788
47DAP/43DAP	1.035	0.989
52DAP/47DAP	1.02417	1
57DAP/52DAP	1.12869	0.971
57DAP/7DAP	0.69716	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.95651	0.445
17DAP/reference	0.93856	0.338
27DAP/reference	0.89841	0.171
39DAP/reference	1.23	0.101
41DAP/reference	0.86636	0.064
42DAP/reference	1.01693	0.791
43DAP/reference	0.92968	0.279
47DAP/reference	1.08677	0.885
52DAP/reference	1.00765	0.621
57DAP/reference	0.95132	0.341

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.81589	0.129
17DAP/reference	0.7425	0.014
27DAP/reference	0.8745	0.111
39DAP/reference	0.98678	0.554
41DAP/reference	0.90061	0.194
42DAP/reference	0.80686	0.05
43DAP/reference	0.74548	0.03
47DAP/reference	0.80483	0.029
52DAP/reference	0.91444	0.203
57DAP/reference	0.71145	0.004

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.94331	0.455
17DAP/reference	0.88317	0.364
27DAP/reference	0.95689	0.376
39DAP/reference	0.98503	0.643
41DAP/reference	1.08369	0.471
42DAP/reference	1.0837	0.743
43DAP/reference	1.03642	0.88
47DAP/reference	0.91039	0.259
52DAP/reference	0.90379	0.415
57DAP/reference	1.2375	0.051

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.99188	1
26DAP/20DAP	1.3279
34DAP/26DAP	1.02966	1
51DAP/34DAP	0.59341	0.097
52DAP/51DAP	0.95015	1
53DAP/52DAP	1.7842	0.552
55DAP/53DAP	1.41151	0.671
57DAP/55DAP	0.70124	0.084
62DAP/57DAP	1.55404	0.047
68DAP/62DAP	1.71759	0.336
68DAP/14DAP	1.81794	0.119

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.696	0.079

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	2.86658
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	N/A	N/A
Mature Eggplant/Ripe Tomato	N/A	N/A

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.96692	0.944
1-1-2/M82	0.91671	1
12-2/M82	0.82688	0.862
12-4/M82	1.08465	1
1-3/M82	0.69289
2-1-1/M82	1.15309	0.689
2-1/M82	N/A	N/A
2-6/M82	1.09281	0.452
3-2/M82	0.99977
4-1-1/M82	1.00994	1
4-1/M82	N/A	N/A
4-3-2/M82	N/A	N/A
4-3/M82	1.35632	1
5-3/M82	0.88292	0.642
6-2/M82	1.14858
6-3/M82	1.04739	1
7-1/M82	1.06371
7-2/M82	1.05505	1
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	2.23684	0.277
IL2-6/WTpooled	0.41033	0.383
IL7-5/WTpooled	1.08448	1
IL7-3/WTpooled	1.18538	1
IL12-4/WTpooled	1.51474	0.516
IL1-4/WTpooled	2.14074	0.426
WT/WTpooled	0.94056	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	0.72382

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.02982	0.921
DC3000/delta hrp 6h	1.09417	1
DC3000/delta hrp 12h	1.32759	1
DC3000/delta hrp 24h	1.10599	0.516

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	0.92496	1
Exp 36h	N/A	N/A
Exp 60h	0.9061	0.994

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

hybridization	ratio	FDR (corrected p value)
self-self	1.01017	1
Var 0h	0.80255	0.457
Var 12h I row2-row1	0.89831	0.705
Var 12h NI row2-row1	0.87755	0.82
Var 36h I row2-row1	0.91353	0.805
Var 36h NI row2-row1	1.14263	0.253
Var 60h I row2-row1	1.01045	1
Var 60h NI row2-row1	1.15616	0.904
Time course 0hI-0hNI	1.29616	0.537
Time course 12hI-12hNI	0.72723	0.149
Time course 36hI-36hNI	0.42725	0.023
Time course 60hI-60hNI	0.2784	0.006

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)	1.342	0.571
transgenic ySAMdc/azygous control (breaker)	0.50591	0.134
transgenic ySAMdc/azygous control (red)	0.97684	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.43024	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.21323	0.105
Manapal/WT (break)	0.94898	1
Manapal/WT (red)	0.86935	0.199