Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.2.12.21

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.96283	0.743
27DAP/17DAP	1.17717	0.872
39DAP/27DAP	1.10164	0.885
41DAP/39DAP	1.20452	0.257
42DAP/41DAP	1.13337	0.962
43DAP/42DAP	1.01538	0.937
47DAP/43DAP	0.77915	0.308
52DAP/47DAP	1.20072	0.649
57DAP/52DAP	1.03666	0.98

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.96818	0.422
17DAP/reference	0.94696	0.074
27DAP/reference	0.89193	0.032
39DAP/reference	1.02186	0.76
41DAP/reference	0.98048	0.667
42DAP/reference	1.07866	0.113
43DAP/reference	0.96741	0.464
47DAP/reference	0.93332	0.09
52DAP/reference	0.87399	0.041
57DAP/reference	0.76075	0.009

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.0673	0.438
27DAP/17DAP	0.96122	0.854
39DAP/27DAP	1.07808	0.478
41DAP/39DAP	0.97152	0.959
42DAP/41DAP	0.97271	0.768
43DAP/42DAP	1.04523	0.554
47DAP/43DAP	1.03341	0.92
52DAP/47DAP	0.97181	0.935
57DAP/52DAP	1.00329	0.921
57DAP/7DAP	0.84718	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.93848	0.168
17DAP/reference	0.95729	0.167
27DAP/reference	0.92358	0.024
39DAP/reference	0.89976	0.012
41DAP/reference	0.87012	0.011
42DAP/reference	0.83984	0.011
43DAP/reference	0.87424	0.012
47DAP/reference	0.91626	0.168
52DAP/reference	0.8958	0.043
57DAP/reference	0.87242	0.011

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.08334	0.33
17DAP/reference	1.06708	0.375
27DAP/reference	1.07178	0.648
39DAP/reference	0.96652	0.392
41DAP/reference	0.86904	0.105
42DAP/reference	1.00476	0.723
43DAP/reference	1.17486	0.096
47DAP/reference	1.11331	0.4
52DAP/reference	1.06102	0.168
57DAP/reference	1.30607	0.078

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.96945	0.455
17DAP/reference	1.03999	0.712
27DAP/reference	0.90303	0.041
39DAP/reference	0.9171	0.018
41DAP/reference	0.95665	0.293
42DAP/reference	0.96425	0.552
43DAP/reference	0.92235	0.237
47DAP/reference	0.98726	0.574
52DAP/reference	0.90894	0.211
57DAP/reference	0.9152	0.238

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.00662	1
26DAP/20DAP	2.12195	0.099
34DAP/26DAP	1.47434	0.542
51DAP/34DAP	0.98816	0.901
52DAP/51DAP	0.94365	1
53DAP/52DAP	1.18947
55DAP/53DAP	0.88469
57DAP/55DAP	0.93497	0.677
62DAP/57DAP	0.99662	1
68DAP/62DAP	1.21704	0.866
68DAP/14DAP	1.07932	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.40097	0.03

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	10.9009	0.058
Mature Green Tomato/Ripe Tomato	0.90376	0.347
Immature Eggplant/Mature Eggplant	14.418	0.05
Ripe Pepper/Ripe Tomato	3.06357	0.256
Mature Eggplant/Ripe Tomato	2.33035	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.03048	1
1-1-2/M82	0.80042	0.804
12-2/M82	1.41379
12-4/M82	1.20139	1
1-3/M82	1.0981	0.479
2-1-1/M82	1.0364	0.764
2-1/M82	N/A	N/A
2-6/M82	1.07094	0.695
3-2/M82	N/A	N/A
4-1-1/M82	1.07463	1
4-1/M82	0.99011	1
4-3-2/M82	0.87106	0.412
4-3/M82	0.99421	1
5-3/M82	1.1531	1
6-2/M82	1.0796	1
6-3/M82	1.03181	1
7-1/M82	N/A	N/A
7-2/M82	1.26744	0.318
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.13677	0.493
IL2-6/WTpooled	0.87323	1
IL7-5/WTpooled	0.97349	1
IL7-3/WTpooled	0.99328	1
IL12-4/WTpooled	1.02284	1
IL1-4/WTpooled	0.88649	0.699
WT/WTpooled	1.02099	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	1.40435	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.02775	0.914
DC3000/delta hrp 6h	1.0428	1
DC3000/delta hrp 12h	1.5303
DC3000/delta hrp 24h	0.99056	1

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.29812	0.068
DC3000 delta B/DC3000 delta AB	1.46422	0.083

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.22342	1
Exp 36h	1.70627	1
Exp 60h	1.34391	1

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

hybridization	ratio	FDR (corrected p value)
self-self	1.00889	1
Var 0h	0.87621	0.933
Var 12h I row2-row1	0.88896	0.565
Var 12h NI row2-row1	1.23505	1
Var 36h I row2-row1	1.01109	1
Var 36h NI row2-row1	0.7994	0.584
Var 60h I row2-row1	0.85949	0.287
Var 60h NI row2-row1	0.84628	0.38
Time course 0hI-0hNI	1.06405	0.719
Time course 12hI-12hNI	1.08762	0.403
Time course 36hI-36hNI	2.0781	0.005
Time course 60hI-60hNI	27.098	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)	0.81643	0.428
transgenic ySAMdc/azygous control (breaker)	0.21593	0.134
transgenic ySAMdc/azygous control (red)	1.71676	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.03934	0.619

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.37843	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	31.6059	0.14
Manapal/WT (break)	1.38691	1
Manapal/WT (red)	2.21771	0.413