Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.1.6.3

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.20191	0.512
27DAP/17DAP	1.29011	0.712
39DAP/27DAP	1.04298	0.899
41DAP/39DAP	0.97647	0.866
42DAP/41DAP	1.24403	0.647
43DAP/42DAP	1.09664	1
47DAP/43DAP	1.46128	0.245
52DAP/47DAP	1.20772	0.566
57DAP/52DAP	0.88566	0.878

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.98373	0.601
17DAP/reference	1.21831	0.033
27DAP/reference	1.08553	0.648
39DAP/reference	1.10335	0.343
41DAP/reference	1.10217	0.393
42DAP/reference	0.96303	0.315
43DAP/reference	0.92821	0.36
47DAP/reference	0.84813	0.027
52DAP/reference	0.76889	0.111
57DAP/reference	0.94367	0.34

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.29117	0.138
27DAP/17DAP	1.14077	0.74
39DAP/27DAP	1.57394	0.082
41DAP/39DAP	0.72105	0.03
42DAP/41DAP	1.1467	0.389
43DAP/42DAP	1.13753	0.324
47DAP/43DAP	0.92731	0.516
52DAP/47DAP	1.16851	0.603
57DAP/52DAP	0.95115	0.641
57DAP/7DAP	1.3626	0.365

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.84391	0.091
17DAP/reference	0.93609	0.253
27DAP/reference	1.01903	1
39DAP/reference	0.99442	0.64
41DAP/reference	0.90132	0.098
42DAP/reference	1.098	0.686
43DAP/reference	1.01238	1
47DAP/reference	1.0102	1
52DAP/reference	0.86098	0.072
57DAP/reference	0.80504	0.016

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.05864	0.794
17DAP/reference	1.43875	0.151
27DAP/reference	1.02824	0.765
39DAP/reference	0.93205	0.37
41DAP/reference	0.97963	0.481
42DAP/reference	0.9141	0.261
43DAP/reference	1.08757	0.624
47DAP/reference	0.96149	0.302
52DAP/reference	0.99331	0.713
57DAP/reference	1.18921	0.051

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.9703	0.489
17DAP/reference	0.93966	0.499
27DAP/reference	0.71201	0.025
39DAP/reference	0.92845	0.36
41DAP/reference	1.01571	0.826
42DAP/reference	1.01344	1
43DAP/reference	1.0852	0.547
47DAP/reference	0.81775	0.231
52DAP/reference	0.91566	0.36
57DAP/reference	0.89951	0.31

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.23354	1
26DAP/20DAP	0.67379	0.244
34DAP/26DAP	1.16501	0.819
51DAP/34DAP	1.35739	0.103
52DAP/51DAP	0.69931	0.151
53DAP/52DAP	1.2945	0.108
55DAP/53DAP	0.86318	0.325
57DAP/55DAP	0.9698	0.872
62DAP/57DAP	N/A	N/A
68DAP/62DAP	1.15839
68DAP/14DAP	0.70509

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.77854	0.068

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.60621	0.072
Immature Eggplant/Mature Eggplant	1.66605
Ripe Pepper/Ripe Tomato	N/A	N/A
Mature Eggplant/Ripe Tomato	1.30187	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.66726	0.591
1-1-2/M82	1.08706	1
12-2/M82	1.18405	1
12-4/M82	1.39283	0.655
1-3/M82	1.55908	0.479
2-1-1/M82	0.93335	0.465
2-1/M82	1.55451	0.345
2-6/M82	1.0752	0.695
3-2/M82	0.99223	1
4-1-1/M82	1.25456	1
4-1/M82	1.26819
4-3-2/M82	1.10731	1
4-3/M82	1.73904	0.268
5-3/M82	1.20843	0.496
6-2/M82	0.99799	1
6-3/M82	1.0127	1
7-1/M82	0.99142	1
7-2/M82	0.98315	1
9-3-2/M82	1.28017	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	N/A	N/A
IL1-4/WTpooled	N/A	N/A
WT/WTpooled	N/A	N/A

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	1.14526	0.479

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.99802	1
DC3000/delta hrp 6h	0.57922
DC3000/delta hrp 12h	1.00627	1
DC3000/delta hrp 24h	0.96912	0.808

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.24974
DC3000 delta B/DC3000 delta AB	1.03511	0.761

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	N/A	N/A
Exp 36h	N/A	N/A
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	1.03492	1
Var 0h	0.86981	0.933
Var 12h I row2-row1	1.13618	0.348
Var 12h NI row2-row1	0.99424	1
Var 36h I row2-row1	1.08872	1
Var 36h NI row2-row1	0.94931	0.791
Var 60h I row2-row1	0.80657	0.832
Var 60h NI row2-row1	1.00428	1
Time course 0hI-0hNI	1.05611	0.63
Time course 12hI-12hNI	0.98052	0.87
Time course 36hI-36hNI	1.04495	1
Time course 60hI-60hNI	1.18099	0.096

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)	0.99607	0.931
transgenic ySAMdc/azygous control (breaker)	1.16982	0.248
transgenic ySAMdc/azygous control (red)	0.90531	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.069	0.11

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.01837	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.87617	1
Manapal/WT (break)	1.07731	0.183
Manapal/WT (red)	0.81602	0.242