Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.4.18.21

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.79924	0.414
27DAP/17DAP	0.9464	0.919
39DAP/27DAP	1.26538	0.787
41DAP/39DAP	1.27803	0.084
42DAP/41DAP	1.08383	0.937
43DAP/42DAP	0.95898	0.898
47DAP/43DAP	1.62607	0.377
52DAP/47DAP	1.20224	0.745
57DAP/52DAP	1.37254	0.955

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.04193	0.567
17DAP/reference	1.14525	0.074
27DAP/reference	1.22803	0.043
39DAP/reference	1.35025	0.058
41DAP/reference	1.27664	0.171
42DAP/reference	0.94133	0.12
43DAP/reference	1.02253	0.866
47DAP/reference	0.99561	0.602
52DAP/reference	1.03144	1
57DAP/reference	1.22	0.259

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.10584	0.858
27DAP/17DAP	1.17452	0.482
39DAP/27DAP	1.00974	0.997
41DAP/39DAP	1.29579	0.579
42DAP/41DAP	0.77756	0.101
43DAP/42DAP	1.17267	0.351
47DAP/43DAP	0.98649	0.919
52DAP/47DAP	0.82544	0.22
57DAP/52DAP	1.14843	0.618
57DAP/7DAP	1.13591	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.88611	0.091
17DAP/reference	1.01834	1
27DAP/reference	1.11184	0.246
39DAP/reference	0.94717	0.264
41DAP/reference	1.09495	0.655
42DAP/reference	1.01554	0.791
43DAP/reference	1.04702	0.788
47DAP/reference	0.93676	0.383
52DAP/reference	1.12672	0.732
57DAP/reference	0.98557	0.53

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.06959	0.634
17DAP/reference	0.97473	0.548
27DAP/reference	1.10654	0.66
39DAP/reference	0.95562	0.392
41DAP/reference	0.95066	0.373
42DAP/reference	1.0504	0.509
43DAP/reference	1.25597	0.173
47DAP/reference	1.00634	1
52DAP/reference	1.06126	0.322
57DAP/reference	1.00939	1

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.84072	0.135
17DAP/reference	1.06666	0.405
27DAP/reference	0.92302	0.657
39DAP/reference	1.13142	0.017
41DAP/reference	1.11507	0.714
42DAP/reference	1.13372	0.627
43DAP/reference	0.86988	0.246
47DAP/reference	1.00305	0.708
52DAP/reference	0.94429	0.472
57DAP/reference	0.97634	0.583

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.12451	0.966
26DAP/20DAP	1.20128	0.642
34DAP/26DAP	1.18185	1
51DAP/34DAP	0.92718	0.703
52DAP/51DAP	1.0161	1
53DAP/52DAP	1.2076	0.678
55DAP/53DAP	1.00143	0.886
57DAP/55DAP	0.91187	0.612
62DAP/57DAP	1.00748	1
68DAP/62DAP	0.67741	0.082
68DAP/14DAP	1.14522	0.739

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.85594	0.358

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.3777
Immature Eggplant/Mature Eggplant	2.04973
Ripe Pepper/Ripe Tomato	1.69994
Mature Eggplant/Ripe Tomato	0.91072

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.8118
1-1-2/M82	1.06971
12-2/M82	N/A	N/A
12-4/M82	1.04017	1
1-3/M82	N/A	N/A
2-1-1/M82	N/A	N/A
2-1/M82	1.10617
2-6/M82	N/A	N/A
3-2/M82	N/A	N/A
4-1-1/M82	N/A	N/A
4-1/M82	N/A	N/A
4-3-2/M82	N/A	N/A
4-3/M82	2.58412
5-3/M82	0.80774	0.369
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	0.94522
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.26808	0.277
IL2-6/WTpooled	0.92297	1
IL7-5/WTpooled	1.17203	0.722
IL7-3/WTpooled	1.3148	0.362
IL12-4/WTpooled	1.14767	0.891
IL1-4/WTpooled	1.06326	1
WT/WTpooled	1.00915	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	1.33406	0.479

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.10749	0.921
DC3000/delta hrp 6h	1.24844
DC3000/delta hrp 12h	1.01432	1
DC3000/delta hrp 24h	0.92904	0.513

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	N/A	N/A
DC3000 delta B/DC3000 delta AB	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	N/A	N/A
Exp 36h	1.38719	1
Exp 60h	1.72982	0.227

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

hybridization	ratio	FDR (corrected p value)
self-self	1.10762	1
Var 0h	0.86406	0.933
Var 12h I row2-row1	1.28127	0.22
Var 12h NI row2-row1	2.43464	1
Var 36h I row2-row1	0.97459	1
Var 36h NI row2-row1	0.81275	0.584
Var 60h I row2-row1	1.06161	1
Var 60h NI row2-row1	1.10794	1
Time course 0hI-0hNI	0.96921	0.833
Time course 12hI-12hNI	1.96058	0.011
Time course 36hI-36hNI	1.67882	0.005
Time course 60hI-60hNI	3.97003	0.011

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)	0.85509	0.222
transgenic ySAMdc/azygous control (breaker)	0.74429	0.15
transgenic ySAMdc/azygous control (red)	0.96176	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.05823	0.061

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.92474	0.431

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.48175	0.307
Manapal/WT (break)	0.76264	0.333
Manapal/WT (red)	0.70837	0.181