Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.2.11.15

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.8396	0.347
27DAP/17DAP	1.17384	0.849
39DAP/27DAP	1.47336	0.179
41DAP/39DAP	1.04477	1
42DAP/41DAP	1.0224	1
43DAP/42DAP	0.9781	0.888
47DAP/43DAP	0.96563	0.828
52DAP/47DAP	1.05058	0.96
57DAP/52DAP	1.05173	0.894

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.06844	0.928
17DAP/reference	0.92778	0.474
27DAP/reference	1.07935	0.637
39DAP/reference	1.10673	0.386
41DAP/reference	0.82041	0.201
42DAP/reference	0.7902	0.069
43DAP/reference	0.99312	0.861
47DAP/reference	0.96386	0.392
52DAP/reference	0.90895	0.115
57DAP/reference	0.94695	0.34

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.20442	0.29
27DAP/17DAP	1.08649	0.653
39DAP/27DAP	1.18642	0.56
41DAP/39DAP	0.98029	0.959
42DAP/41DAP	1.04622	0.927
43DAP/42DAP	0.90171	0.431
47DAP/43DAP	1.04462	0.906
52DAP/47DAP	1.03341	0.987
57DAP/52DAP	1.15195	0.571
57DAP/7DAP	1.12122	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.96976	0.495
17DAP/reference	0.83853	0.014
27DAP/reference	0.84232	0.011
39DAP/reference	0.83353	0.011
41DAP/reference	0.83296	0.024
42DAP/reference	0.97901	0.531
43DAP/reference	0.76472	0.027
47DAP/reference	0.91292	0.504
52DAP/reference	0.81136	0.023
57DAP/reference	0.85181	0.071

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.97089	0.639
17DAP/reference	0.86055	0.034
27DAP/reference	0.81071	0.229
39DAP/reference	0.89479	0.339
41DAP/reference	0.86638	0.231
42DAP/reference	1.01223	1
43DAP/reference	0.89945	0.378
47DAP/reference	0.9481	0.459
52DAP/reference	1.23683	0.168
57DAP/reference	0.88187	0.054

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.88937	0.059
17DAP/reference	0.9887	0.709
27DAP/reference	0.78219	0.031
39DAP/reference	0.86923	0.076
41DAP/reference	0.75068	0.035
42DAP/reference	0.9204	0.059
43DAP/reference	0.95248	0.334
47DAP/reference	1.04151	1
52DAP/reference	0.95102	0.582
57DAP/reference	0.95031	0.543

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.0999	0.966
26DAP/20DAP	1.04283	1
34DAP/26DAP	0.99316	0.998
51DAP/34DAP	1.32592	0.032
52DAP/51DAP	0.88847	1
53DAP/52DAP	1.10834	0.489
55DAP/53DAP	0.83488	0.14
57DAP/55DAP	1.03505	0.904
62DAP/57DAP	0.79434	0.028
68DAP/62DAP	1.19861	0.5
68DAP/14DAP	1.27494	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.03066	0.696

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	1.12457	0.898
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	N/A	N/A
Mature Eggplant/Ripe Tomato	0.97705

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	0.9067
12-2/M82	N/A	N/A
12-4/M82	1.03255	1
1-3/M82	N/A	N/A
2-1-1/M82	0.69292
2-1/M82	N/A	N/A
2-6/M82	N/A	N/A
3-2/M82	0.88048
4-1-1/M82	N/A	N/A
4-1/M82	0.94937	1
4-3-2/M82	1.09896	1
4-3/M82	1.14391
5-3/M82	1.05462	1
6-2/M82	N/A	N/A
6-3/M82	0.90536	0.982
7-1/M82	N/A	N/A
7-2/M82	N/A	N/A
9-3-2/M82	1.06395

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	1.26469	0.531
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.66609	0.418
IL12-4/WTpooled	0.80779	0.554
IL1-4/WTpooled	1.20894	1
WT/WTpooled	1.04762	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	1.03644	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	N/A	N/A
DC3000/delta hrp 6h	0.64328	0.95
DC3000/delta hrp 12h	1.0064	1
DC3000/delta hrp 24h	0.77616	0.071

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.35606
DC3000 delta B/DC3000 delta AB	1.37323	0.126

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.80765	1
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	1.03598	1
Var 0h	0.67775	1
Var 12h I row2-row1	0.99976	1
Var 12h NI row2-row1	1.11343	0.266
Var 36h I row2-row1	1.25263	0.304
Var 36h NI row2-row1	0.90228	0.378
Var 60h I row2-row1	0.76951	0.439
Var 60h NI row2-row1	0.95411	1
Time course 0hI-0hNI	0.96653	0.839
Time course 12hI-12hNI	0.99579	1
Time course 36hI-36hNI	1.10255	0.023
Time course 60hI-60hNI	1.39362	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)	1.088	0.297
transgenic ySAMdc/azygous control (breaker)	1.68385	0.165
transgenic ySAMdc/azygous control (red)	1.12669	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.69465	0.191

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.49075	0.307
Manapal/WT (break)	1.5042	0.14
Manapal/WT (red)	1.03771	1