Tomato Functional Genomics Database (TFGD)

Expression of 1-1-6.2.11.17

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.10243	0.739
27DAP/17DAP	1.04717	0.927
39DAP/27DAP	1.05531	1
41DAP/39DAP	1.55322	0.25
42DAP/41DAP	1.09499	1
43DAP/42DAP	0.96194	0.909
47DAP/43DAP	1.135	0.825
52DAP/47DAP	1.40346	0.418
57DAP/52DAP	0.84731	0.707

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.93162	0.162
17DAP/reference	1.00125	1
27DAP/reference	0.97592	0.514
39DAP/reference	1.06234	0.086
41DAP/reference	0.98904	0.814
42DAP/reference	0.8929	0.017
43DAP/reference	1.02505	0.705
47DAP/reference	0.91166	0.009
52DAP/reference	0.89529	0.135
57DAP/reference	0.84802	0.096

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.95714	0.613
27DAP/17DAP	0.96331	0.854
39DAP/27DAP	1.14713	0.359
41DAP/39DAP	1.02682	1
42DAP/41DAP	1.07389	0.74
43DAP/42DAP	1.05703	0.513
47DAP/43DAP	1.11951	0.344
52DAP/47DAP	0.9814	0.913
57DAP/52DAP	1.0307	0.877
57DAP/7DAP	1.26191	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.9152	0.062
17DAP/reference	0.94821	0.017
27DAP/reference	0.99846	0.8
39DAP/reference	0.96169	0.025
41DAP/reference	0.92705	0.07
42DAP/reference	0.91862	0.082
43DAP/reference	0.90753	0.044
47DAP/reference	0.95052	0.293
52DAP/reference	0.89425	0.066
57DAP/reference	0.88405	0.033

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.018	0.894
17DAP/reference	0.96723	0.461
27DAP/reference	0.8861	0.16
39DAP/reference	0.87985	0.152
41DAP/reference	0.80133	0.045
42DAP/reference	0.95498	0.433
43DAP/reference	1.107	0.255
47DAP/reference	1.06242	0.4
52DAP/reference	0.9989	0.713
57DAP/reference	1.10947	0.052

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.95722	0.077
17DAP/reference	1.02344	0.563
27DAP/reference	0.98078	0.465
39DAP/reference	0.97549	0.43
41DAP/reference	0.95871	0.037
42DAP/reference	1.0052	1
43DAP/reference	0.92464	0.319
47DAP/reference	1.01645	1
52DAP/reference	1.06968	0.393
57DAP/reference	0.71842	0.034

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.0293	0.966
26DAP/20DAP	0.99379	1
34DAP/26DAP	1.05095	1
51DAP/34DAP	0.89681	0.23
52DAP/51DAP	1.03171	0.808
53DAP/52DAP	0.99298	0.938
55DAP/53DAP	1.10923	0.689
57DAP/55DAP	0.96799	0.825
62DAP/57DAP	1.12807	0.767
68DAP/62DAP	1.1316	0.914
68DAP/14DAP	1.01793	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.0516	0.814

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.80911	0.312
Mature Green Tomato/Ripe Tomato	0.96846	0.66
Immature Eggplant/Mature Eggplant	1.58963	0.078
Ripe Pepper/Ripe Tomato	1.10634	1
Mature Eggplant/Ripe Tomato	0.33596	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.09134	1
1-1-2/M82	0.94628	1
12-2/M82	1.0234	1
12-4/M82	0.94267	1
1-3/M82	0.97327	1
2-1-1/M82	1.09147	0.764
2-1/M82	1.04103
2-6/M82	0.95294	1
3-2/M82	1.01011	1
4-1-1/M82	1.07324	1
4-1/M82	0.91764
4-3-2/M82	0.93732	1
4-3/M82	1.01784	1
5-3/M82	1.00782	1
6-2/M82	0.96131	1
6-3/M82	0.98169	1
7-1/M82	0.97425	0.509
7-2/M82	1.00755	1
9-3-2/M82	0.89698	0.449

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	0.65513	0.473
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.02483	1
IL12-4/WTpooled	0.93966	1
IL1-4/WTpooled	1.06674	1
WT/WTpooled	0.99458	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	1.06693	0.479

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.07277	0.894
DC3000/delta hrp 6h	1.19845	1
DC3000/delta hrp 12h	0.8992	1
DC3000/delta hrp 24h	0.95961	0.7

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.0064
DC3000 delta B/DC3000 delta AB	1.00479	1

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.09446	1
Exp 36h	1.11008	0.693
Exp 60h	1.12669	1

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

hybridization	ratio	FDR (corrected p value)
self-self	1.03636	1
Var 0h	0.99842	1
Var 12h I row2-row1	1.13691	0.201
Var 12h NI row2-row1	0.99072	1
Var 36h I row2-row1	1.14726	1
Var 36h NI row2-row1	0.85259	0.61
Var 60h I row2-row1	1.19614	1
Var 60h NI row2-row1	1.12488	1
Time course 0hI-0hNI	1.12837	0.63
Time course 12hI-12hNI	1.01732	0.868
Time course 36hI-36hNI	1.0477	0.248
Time course 60hI-60hNI	1.34447	0.012

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)	0.9541	0.33
transgenic ySAMdc/azygous control (breaker)	1.227	0.178
transgenic ySAMdc/azygous control (red)	0.92493	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.02436	0.301

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.88481	0.241

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.86314	1
Manapal/WT (break)	1.13114	0.381
Manapal/WT (red)	0.78662	0.181