Tomato Functional Genomics Database (TFGD)

Expression of 1-1-8.2.15.12

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.92102	0.558
27DAP/17DAP	1.31543	0.793
39DAP/27DAP	0.84175	0.522
41DAP/39DAP	1.32407	0.442
42DAP/41DAP	0.87132	1
43DAP/42DAP	0.96373	0.909
47DAP/43DAP	0.97962	0.876
52DAP/47DAP	1.20856	0.615
57DAP/52DAP	1.08434	0.946

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.98844	0.645
17DAP/reference	0.98738	0.701
27DAP/reference	1.04107	0.66
39DAP/reference	1.00011	1
41DAP/reference	0.91791	0.201
42DAP/reference	0.94127	0.035
43DAP/reference	1.03761	0.518
47DAP/reference	0.97574	0.345
52DAP/reference	0.82744	0.03
57DAP/reference	0.93808	0.038

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.96554	0.578
27DAP/17DAP	0.95444	0.854
39DAP/27DAP	1.0774	0.548
41DAP/39DAP	0.99848	1
42DAP/41DAP	1.00992	0.932
43DAP/42DAP	0.98253	0.751
47DAP/43DAP	1.01284	0.934
52DAP/47DAP	0.98764	0.93
57DAP/52DAP	1.01909	0.925
57DAP/7DAP	1.05332	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.95469	0.072
17DAP/reference	0.96928	0.167
27DAP/reference	0.95615	0.048
39DAP/reference	1.0516	0.09
41DAP/reference	1.00064	0.848
42DAP/reference	1.04613	0.686
43DAP/reference	1.09026	0.226
47DAP/reference	1.00204	1
52DAP/reference	1.05052	0.459
57DAP/reference	0.96559	0.123

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.01513	0.894
17DAP/reference	1.01264	0.979
27DAP/reference	0.90879	0.181
39DAP/reference	0.88901	0.102
41DAP/reference	0.95087	0.299
42DAP/reference	0.9918	0.655
43DAP/reference	0.92453	0.328
47DAP/reference	0.99984	0.77
52DAP/reference	0.95589	0.259
57DAP/reference	1.00899	1

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.97668	0.268
17DAP/reference	0.96196	0.537
27DAP/reference	0.98725	0.376
39DAP/reference	0.96577	0.04
41DAP/reference	0.98528	0.618
42DAP/reference	0.94363	0.361
43DAP/reference	0.94435	0.294
47DAP/reference	0.94501	0.348
52DAP/reference	0.9863	0.763
57DAP/reference	0.74457	0.021

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.98013	1
26DAP/20DAP	1.08183	0.826
34DAP/26DAP	0.95586	0.771
51DAP/34DAP	0.94678	0.703
52DAP/51DAP	1.03265	0.704
53DAP/52DAP	0.79251	0.207
55DAP/53DAP	1.05727	0.869
57DAP/55DAP	0.98682	0.823
62DAP/57DAP	1.08932	0.935
68DAP/62DAP	1.10418	0.912
68DAP/14DAP	0.8126	0.375

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.9898	0.696

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.18118	0.058
Mature Green Tomato/Ripe Tomato	1.01663	1
Immature Eggplant/Mature Eggplant	1.1394	0.157
Ripe Pepper/Ripe Tomato	0.83659	0.293
Mature Eggplant/Ripe Tomato	1.43212	0.373

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.00159	1
1-1-2/M82	0.96797	1
12-2/M82	1.15721	0.519
12-4/M82	0.92748	1
1-3/M82	0.89933	0.378
2-1-1/M82	1.28522	0.764
2-1/M82	1.41395
2-6/M82	1.01493	1
3-2/M82	0.97568	1
4-1-1/M82	0.90046	1
4-1/M82	0.75174
4-3-2/M82	0.86804	1
4-3/M82	0.96727	1
5-3/M82	1.06174	1
6-2/M82	1.08381
6-3/M82	1.09036	1
7-1/M82	1.0736	0.598
7-2/M82	1.02356	1
9-3-2/M82	0.84923	0.449

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	2.49244	0.441
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.9754
IL12-4/WTpooled	1.2397	0.553
IL1-4/WTpooled	1.08176	0.426
WT/WTpooled	1.00647	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	1.26536	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.933	1
DC3000/delta hrp 6h	1.01514	0.95
DC3000/delta hrp 12h	1.06072	1
DC3000/delta hrp 24h	1.00108	1

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.07421	0.25
DC3000 delta B/DC3000 delta AB	1.08966	0.381

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.25803	1
Exp 36h	1.09777	1
Exp 60h	1.20549	0.563

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

hybridization	ratio	FDR (corrected p value)
self-self	1.0031	1
Var 0h	0.99891	1
Var 12h I row2-row1	1.06198	0.654
Var 12h NI row2-row1	0.93784	0.82
Var 36h I row2-row1	0.99147	1
Var 36h NI row2-row1	0.89793	0.421
Var 60h I row2-row1	1.05868	1
Var 60h NI row2-row1	1.05736	1
Time course 0hI-0hNI	1.09453	0.833
Time course 12hI-12hNI	1.01819	0.88
Time course 36hI-36hNI	1.07391	0.039
Time course 60hI-60hNI	1.66103	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)	1.18624	0.384
transgenic ySAMdc/azygous control (breaker)	0.84075	0.251
transgenic ySAMdc/azygous control (red)	0.98883	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.00011	1

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.77005	0.241

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.89616	1
Manapal/WT (break)	1.2102	0.381
Manapal/WT (red)	0.89994	0.424