Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.4.7.17

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.03819	1
27DAP/17DAP	0.97366	0.982
39DAP/27DAP	0.84172	0.39
41DAP/39DAP	1.10092	0.806
42DAP/41DAP	1.02775	1
43DAP/42DAP	0.911	0.834
47DAP/43DAP	1.07137	0.809
52DAP/47DAP	0.9231	0.765
57DAP/52DAP	1.08825	0.977

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.99389	0.693
17DAP/reference	1.19524	0.083
27DAP/reference	1.02854	0.847
39DAP/reference	1.07652	0.423
41DAP/reference	1.2074	0.03
42DAP/reference	0.96474	0.233
43DAP/reference	0.97617	0.728
47DAP/reference	0.98849	0.535
52DAP/reference	0.92671	0.189
57DAP/reference	0.89161	0.131

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.01824	0.91
27DAP/17DAP	1.0019	1
39DAP/27DAP	1.00129	1
41DAP/39DAP	1.04448	0.799
42DAP/41DAP	0.8385	0.196
43DAP/42DAP	1.00001	1
47DAP/43DAP	0.97904	0.833
52DAP/47DAP	0.98861	0.935
57DAP/52DAP	0.98202	0.745
57DAP/7DAP	1.00755	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.15002
17DAP/reference	0.93749	0.025
27DAP/reference	0.91369	0.011
39DAP/reference	0.95535	0.083
41DAP/reference	0.95661	0.203
42DAP/reference	0.95117	0.046
43DAP/reference	0.92347	0.022
47DAP/reference	0.88247	0.168
52DAP/reference	0.95519	0.163
57DAP/reference	0.92398	0.156

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.96294	0.607
17DAP/reference	1.0694	0.357
27DAP/reference	0.97894	0.537
39DAP/reference	0.81163	0.168
41DAP/reference	0.9472	0.322
42DAP/reference	0.9189	0.237
43DAP/reference	1.13746	0.59
47DAP/reference	0.97142	0.368
52DAP/reference	1.06074	0.343
57DAP/reference	1.25579	0.01

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.95309	0.311
17DAP/reference	1.04081	0.685
27DAP/reference	1.14563	0.695
39DAP/reference	0.91984	0.05
41DAP/reference	0.95452	0.371
42DAP/reference	0.91422	0.22
43DAP/reference	0.79236	0.068
47DAP/reference	1.05927	0.585
52DAP/reference	0.87286	0.155
57DAP/reference	0.72731	0.02

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.8732	0.807
26DAP/20DAP	0.95356	1
34DAP/26DAP	1.00115	1
51DAP/34DAP	0.95823	0.681
52DAP/51DAP	1.0223	0.792
53DAP/52DAP	1.05702	0.806
55DAP/53DAP	1.02703	0.976
57DAP/55DAP	0.97849	0.911
62DAP/57DAP	1.04766	0.833
68DAP/62DAP	0.78444	0.406
68DAP/14DAP	0.894	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.97524	0.576

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.81363	0.377
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	0.52762	0.224
Mature Eggplant/Ripe Tomato	1.43039	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.97234	0.961
1-1-2/M82	1.03116	1
12-2/M82	1.02426	1
12-4/M82	0.84803	1
1-3/M82	1.07411
2-1-1/M82	1.1272	0.764
2-1/M82	N/A	N/A
2-6/M82	0.94462	0.501
3-2/M82	0.96805	1
4-1-1/M82	0.84868
4-1/M82	0.72894
4-3-2/M82	1.0225
4-3/M82	1.02015	1
5-3/M82	1.02694	1
6-2/M82	1.01603	1
6-3/M82	1.10723
7-1/M82	0.92898	0.803
7-2/M82	0.90743
9-3-2/M82	0.82397	0.449

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.04229
IL2-6/WTpooled	1.06459	0.659
IL7-5/WTpooled	1.70845
IL7-3/WTpooled	1.06727	0.362
IL12-4/WTpooled	1.14125	0.531
IL1-4/WTpooled	0.97984
WT/WTpooled	0.99677	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	1.00136	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.02318	0.921
DC3000/delta hrp 6h	N/A	N/A
DC3000/delta hrp 12h	1.13596	1
DC3000/delta hrp 24h	0.99499	1

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.04017	0.515
DC3000 delta B/DC3000 delta AB	1.01406	0.694

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	N/A	N/A
Exp 36h	2.90687	1
Exp 60h	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
self-self	0.97753	1
Var 0h	N/A	N/A
Var 12h I row2-row1	1.18697	0.22
Var 12h NI row2-row1	0.96642	0.906
Var 36h I row2-row1	0.98154	1
Var 36h NI row2-row1	0.91057	0.61
Var 60h I row2-row1	1.09832	1
Var 60h NI row2-row1	1.08725	1
Time course 0hI-0hNI	1.06275	0.833
Time course 12hI-12hNI	0.99658	1
Time course 36hI-36hNI	1.0315	0.513
Time course 60hI-60hNI	1.36748	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)	0.90669	0.301
transgenic ySAMdc/azygous control (breaker)	1.1538	0.248
transgenic ySAMdc/azygous control (red)	0.91149	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.97312	0.27

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.91613	0.789

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.91423	1
Manapal/WT (break)	0.94878	1
Manapal/WT (red)	1.33043	0.222