Tomato Functional Genomics Database (TFGD)

Expression of 1-1-8.3.5.4

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.74573	0.221
27DAP/17DAP	0.72586	0.135
39DAP/27DAP	0.59615	0.335
41DAP/39DAP	0.92417	0.685
42DAP/41DAP	0.9397	1
43DAP/42DAP	1.06378	1
47DAP/43DAP	0.52324	0.055
52DAP/47DAP	1.16335	0.813
57DAP/52DAP	1.20018	0.977

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.08505	0.685
17DAP/reference	0.86155	0.046
27DAP/reference	0.88347	0.147
39DAP/reference	0.93116	0.284
41DAP/reference	0.89363	0.341
42DAP/reference	0.81006	0.034
43DAP/reference	0.92286	0.464
47DAP/reference	0.8541	0.161
52DAP/reference	0.8254	0.065
57DAP/reference	1.05793	0.478

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.86906	0.185
27DAP/17DAP	0.89395	0.614
39DAP/27DAP	0.56498	0.035
41DAP/39DAP	1.00522	1
42DAP/41DAP	0.97161	0.737
43DAP/42DAP	0.5325	0.022
47DAP/43DAP	0.82088	0.211
52DAP/47DAP	1.08286	0.862
57DAP/52DAP	0.86477	0.476
57DAP/7DAP	0.52084	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.02355	0.813
17DAP/reference	0.84208	0.094
27DAP/reference	0.89235	0.033
39DAP/reference	0.8257	0.027
41DAP/reference	0.79467	0.032
42DAP/reference	0.76767	0.026
43DAP/reference	0.65391	0.013
47DAP/reference	1.01053	0.671
52DAP/reference	0.69389	0.017
57DAP/reference	0.71631	0.02

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.08802	0.719
17DAP/reference	0.82403	0.077
27DAP/reference	0.90882	0.282
39DAP/reference	0.83797	0.102
41DAP/reference	1.00795	0.735
42DAP/reference	0.96825	0.355
43DAP/reference	0.97761	0.62
47DAP/reference	0.84094	0.081
52DAP/reference	0.64736	0.007
57DAP/reference	0.8433	0.004

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.05464	0.575
17DAP/reference	1.07026	0.111
27DAP/reference	0.95126	0.319
39DAP/reference	0.8372	0.017
41DAP/reference	0.91992	0.209
42DAP/reference	0.8088	0.041
43DAP/reference	0.81295	0.061
47DAP/reference	0.73689	0.017
52DAP/reference	0.71436	0.089
57DAP/reference	1.22542	0.223

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.11609	1
26DAP/20DAP	1.31606	0.735
34DAP/26DAP	0.86458	0.816
51DAP/34DAP	1.37565	0.062
52DAP/51DAP	0.78502
53DAP/52DAP	0.88538	0.505
55DAP/53DAP	0.55437	0.017
57DAP/55DAP	1.65868	0.525
62DAP/57DAP	1.11897	0.003
68DAP/62DAP	1.23649	0.193
68DAP/14DAP	1.32702	0.249

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.20044	0.019

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.18246
Mature Green Tomato/Ripe Tomato	5.48116	0.015
Immature Eggplant/Mature Eggplant	1.64353	0.278
Ripe Pepper/Ripe Tomato	N/A	N/A
Mature Eggplant/Ripe Tomato	4.06667

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	N/A	N/A
12-2/M82	N/A	N/A
12-4/M82	N/A	N/A
1-3/M82	N/A	N/A
2-1-1/M82	N/A	N/A
2-1/M82	N/A	N/A
2-6/M82	N/A	N/A
3-2/M82	0.71503
4-1-1/M82	N/A	N/A
4-1/M82	N/A	N/A
4-3-2/M82	2.40368
4-3/M82	N/A	N/A
5-3/M82	N/A	N/A
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	0.9072
7-2/M82	N/A	N/A
9-3-2/M82	1.21961

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.39461	0.277
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	0.51327
IL1-4/WTpooled	1.12627
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	0.94954	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.20326	0.846
DC3000/delta hrp 6h	0.75034	0.743
DC3000/delta hrp 12h	0.95853	1
DC3000/delta hrp 24h	1.25353	0.76

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.56446	0.033
DC3000 delta B/DC3000 delta AB	0.63631	0.025

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.08441	1
Exp 36h	1.58236	1
Exp 60h	1.18395	1

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

hybridization	ratio	FDR (corrected p value)
self-self	1.05349	1
Var 0h	1.18346	1
Var 12h I row2-row1	0.72839	0.338
Var 12h NI row2-row1	0.89845	0.36
Var 36h I row2-row1	0.75789	0.805
Var 36h NI row2-row1	1.19717	0.482
Var 60h I row2-row1	0.99131	1
Var 60h NI row2-row1	0.94641	0.932
Time course 0hI-0hNI	0.99141	1
Time course 12hI-12hNI	1.01022	1
Time course 36hI-36hNI	0.91028	0.108
Time course 60hI-60hNI	0.14557	0.005

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)	1.00514	0.921
transgenic ySAMdc/azygous control (breaker)	1.5561	0.248
transgenic ySAMdc/azygous control (red)	0.97679	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.00423	0.766

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)	1.09937	0.307
Manapal/WT (break)	0.83484	1
Manapal/WT (red)	N/A	N/A