Tomato Functional Genomics Database (TFGD)

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Expression of 1-1-6.1.18.1

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.97721	0.801
27DAP/17DAP	1.21859	0.833
39DAP/27DAP	1.3947	0.225
41DAP/39DAP	0.96411	0.849
42DAP/41DAP	1.14782	0.938
43DAP/42DAP	1.12822	1
47DAP/43DAP	1.04436	0.909
52DAP/47DAP	1.02821	0.848
57DAP/52DAP	1.01476	0.983

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.10474	0.334
17DAP/reference	0.94159	0.448
27DAP/reference	0.97072	0.61
39DAP/reference	0.96719	0.651
41DAP/reference	0.85034	0.039
42DAP/reference	1.00436	0.645
43DAP/reference	0.96492	0.48
47DAP/reference	0.99237	0.568
52DAP/reference	1.06305	1
57DAP/reference	0.99392	0.671

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.96716	0.629
27DAP/17DAP	1.03986	0.957
39DAP/27DAP	1.14905	0.496
41DAP/39DAP	1.2594	0.55
42DAP/41DAP	0.92844	0.52
43DAP/42DAP	1.03062	0.83
47DAP/43DAP	0.9197	0.534
52DAP/47DAP	0.9107	0.617
57DAP/52DAP	0.99175	0.838
57DAP/7DAP	1.91337	0.365

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.86938	0.246
17DAP/reference	0.78254	0.021
27DAP/reference	0.73934	0.01
39DAP/reference	0.79852	0.016
41DAP/reference	0.73442	0.018
42DAP/reference	0.73436	0.01
43DAP/reference	0.75471	0.019
47DAP/reference	0.84979	0.168
52DAP/reference	0.82056	0.04
57DAP/reference	0.81491	0.031

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.10147	0.495
17DAP/reference	0.92817	0.269
27DAP/reference	1.23809	0.053
39DAP/reference	1.20309	0.309
41DAP/reference	1.0335	1
42DAP/reference	0.89842	0.237
43DAP/reference	1.13268	0.435
47DAP/reference	0.94961	0.284
52DAP/reference	1.04535	0.528
57DAP/reference	1.11919	0.724

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.69569	0.039
17DAP/reference	0.89822	0.342
27DAP/reference	0.68027	0.03
39DAP/reference	0.68	0.008
41DAP/reference	0.81533	0.043
42DAP/reference	0.76468	0.041
43DAP/reference	0.81683	0.102
47DAP/reference	1.04292	1
52DAP/reference	0.77438	0.153
57DAP/reference	1.05021	0.878

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.09149	0.966
26DAP/20DAP	1.14052	0.66
34DAP/26DAP	0.8915	0.702
51DAP/34DAP	0.9123	0.394
52DAP/51DAP	1.01506	1
53DAP/52DAP	1.15406	0.678
55DAP/53DAP	1.05063	1
57DAP/55DAP	1.28809	0.793
62DAP/57DAP	0.81576	0.162
68DAP/62DAP	1.03783	0.991
68DAP/14DAP	0.83403	0.375

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.10858	0.14

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.3769	0.059
Mature Green Tomato/Ripe Tomato	0.956	0.611
Immature Eggplant/Mature Eggplant	1.65502	0.05
Ripe Pepper/Ripe Tomato	0.6258	0.224
Mature Eggplant/Ripe Tomato	0.93259	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.07215	0.5
1-1-2/M82	0.94029	0.958
12-2/M82	0.86449	N/A
12-4/M82	1.18587	1
1-3/M82	1.06967	N/A
2-1-1/M82	0.87972	0.465
2-1/M82	0.9982	1
2-6/M82	0.9678	N/A
3-2/M82	0.908	N/A
4-1-1/M82	0.70936	N/A
4-1/M82	1.16309	0.853
4-3-2/M82	N/A	N/A
4-3/M82	0.97639	1
5-3/M82	1.08765	1
6-2/M82	1.06288	1
6-3/M82	0.98673	1
7-1/M82	1.63592	N/A
7-2/M82	0.92323	N/A
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	2.51267	0.277
IL2-6/WTpooled	0.91655	1
IL7-5/WTpooled	1.0053	1
IL7-3/WTpooled	3.03907	1
IL12-4/WTpooled	1.44226	0.516
IL1-4/WTpooled	2.31788	1
WT/WTpooled	0.96044	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	0.86816	0.497

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.9056	1
DC3000/delta hrp 6h	0.99124	0.95
DC3000/delta hrp 12h	1.12699	1
DC3000/delta hrp 24h	0.96468	0.761

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.88691	N/A
DC3000 delta B/DC3000 delta AB	1.44711	0.389

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	N/A	N/A
Exp 36h	1.17737	1
Exp 60h	1.06993	1

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

hybridization	ratio	FDR (corrected p value)
self-self	1.06966	1
Var 0h	0.70532	0.244
Var 12h I row2-row1	1.03034	0.654
Var 12h NI row2-row1	1.0578	1
Var 36h I row2-row1	0.9669	1
Var 36h NI row2-row1	0.97078	0.791
Var 60h I row2-row1	0.94182	0.832
Var 60h NI row2-row1	0.99664	1
Time course 0hI-0hNI	1.11613	0.719
Time course 12hI-12hNI	1.04848	0.754
Time course 36hI-36hNI	0.9401	0.202
Time course 60hI-60hNI	1.15278	0.115

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)	1.0993	0.384
transgenic ySAMdc/azygous control (breaker)	0.47919	0.122
transgenic ySAMdc/azygous control (red)	0.91487	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.15849	0.035

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.68847	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.95374	1
Manapal/WT (break)	0.77987	0.297
Manapal/WT (red)	0.78448	0.181