Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.4.13.8

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.0748	0.681
27DAP/17DAP	1.0073	1
39DAP/27DAP	0.9889	0.782
41DAP/39DAP	1.37461	0.273
42DAP/41DAP	1.1487	0.868
43DAP/42DAP	0.9876	0.932
47DAP/43DAP	0.88546	0.618
52DAP/47DAP	1.12698	0.776
57DAP/52DAP	1.06755	0.92

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.94785	0.194
17DAP/reference	0.98929	0.737
27DAP/reference	0.97136	0.428
39DAP/reference	0.96883	0.638
41DAP/reference	0.86895	0.154
42DAP/reference	0.82166	0.01
43DAP/reference	0.94329	0.273
47DAP/reference	0.89784	0.008
52DAP/reference	0.90719	0.25
57DAP/reference	0.94096	0.395

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.02613	0.708
27DAP/17DAP	0.99475	0.943
39DAP/27DAP	1.00439	0.862
41DAP/39DAP	0.98332	0.997
42DAP/41DAP	0.99648	0.924
43DAP/42DAP	0.99008	0.854
47DAP/43DAP	3.88513	0.708
52DAP/47DAP	0.94472	0.6
57DAP/52DAP	0.97639	0.56
57DAP/7DAP	1.13008	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.89216	0.082
17DAP/reference	0.90293	0.014
27DAP/reference	0.91526	0.082
39DAP/reference	0.99354	0.64
41DAP/reference	1.01802	0.891
42DAP/reference	1.00657	1
43DAP/reference	0.89669	0.166
47DAP/reference	0.87226	0.168
52DAP/reference	0.87536	0.053
57DAP/reference	0.91892	0.077

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.9066	0.09
17DAP/reference	0.9134	0.059
27DAP/reference	0.86212	0.123
39DAP/reference	0.85376	0.093
41DAP/reference	0.82906	0.054
42DAP/reference	0.85461	0.024
43DAP/reference	0.91906	0.152
47DAP/reference	0.96234	0.123
52DAP/reference	0.9033	0.043
57DAP/reference	0.95475	0.298

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.94333	0.047
17DAP/reference	0.90118	0.214
27DAP/reference	0.88198	0.027
39DAP/reference	0.93148	0.033
41DAP/reference	0.87289	0.132
42DAP/reference	0.80252	0.02
43DAP/reference	0.80234	0.066
47DAP/reference	0.92703	0.231
52DAP/reference	0.9088	0.385
57DAP/reference	0.74201	0.022

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.08649	0.85
26DAP/20DAP	0.98754	1
34DAP/26DAP	1.07858	0.542
51DAP/34DAP	1.00228	1
52DAP/51DAP	0.97287	1
53DAP/52DAP	1.1003	0.712
55DAP/53DAP	0.91516	0.181
57DAP/55DAP	1.2376	0.805
62DAP/57DAP	0.94878	0.871
68DAP/62DAP	1.16213	0.253
68DAP/14DAP	1.05679	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.07202	0.347

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	2.8194	0.059
Mature Green Tomato/Ripe Tomato	1.4541	0.331
Immature Eggplant/Mature Eggplant	1.8089	0.07
Ripe Pepper/Ripe Tomato	0.66658	0.224
Mature Eggplant/Ripe Tomato	0.3486	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.88978	0.883
1-1-2/M82	0.967	1
12-2/M82	0.96583	0.955
12-4/M82	0.90833	1
1-3/M82	0.89209	0.501
2-1-1/M82	0.94833	0.92
2-1/M82	1.06432	1
2-6/M82	0.91603	1
3-2/M82	0.91577	1
4-1-1/M82	0.9619	1
4-1/M82	0.73715	1
4-3-2/M82	0.68647	0.487
4-3/M82	0.86914	0.72
5-3/M82	1.04111	1
6-2/M82	0.98348	0.497
6-3/M82	1.06303	1
7-1/M82	1.02069	1
7-2/M82	0.94589	0.599
9-3-2/M82	0.81929	0.355

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.15082	0.493
IL2-6/WTpooled	1.09268	0.46
IL7-5/WTpooled	1.46422
IL7-3/WTpooled	1.00118	1
IL12-4/WTpooled	1.07388	0.557
IL1-4/WTpooled	1.01858	1
WT/WTpooled	1.10056	0.999

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	0.86256	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.05124	0.692
DC3000/delta hrp 6h	0.98991	0.95
DC3000/delta hrp 12h	0.95014	1
DC3000/delta hrp 24h	0.79685

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.9898	1
DC3000 delta B/DC3000 delta AB	1.0177	0.703

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.09266	1
Exp 36h	0.92413	0.82
Exp 60h	0.97294	0.994

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

hybridization	ratio	FDR (corrected p value)
self-self	1.01806	1
Var 0h	1.12883	1
Var 12h I row2-row1	1.22941	0.19
Var 12h NI row2-row1	1.01312	1
Var 36h I row2-row1	0.87439	1
Var 36h NI row2-row1	1.61235	1
Var 60h I row2-row1	1.14931	0.562
Var 60h NI row2-row1	1.01464	1
Time course 0hI-0hNI	1.05522	0.799
Time course 12hI-12hNI	0.95161	0.562
Time course 36hI-36hNI	0.88162	0.049
Time course 60hI-60hNI	0.82696	0.026

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)	1.01193	1
transgenic ySAMdc/azygous control (breaker)	0.85009	0.139
transgenic ySAMdc/azygous control (red)	0.98286	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.97525	0.196

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.94734	0.431

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.63618	0.172
Manapal/WT (break)	1.10045	1
Manapal/WT (red)	0.82051	0.216