Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.4.19.18

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.9499	0.743
27DAP/17DAP	1.26097	0.847
39DAP/27DAP	1.54422	0.212
41DAP/39DAP	0.94069	0.777
42DAP/41DAP	1.07773	0.997
43DAP/42DAP	1.04295	0.937
47DAP/43DAP	0.93418	0.625
52DAP/47DAP	1.14971	0.964
57DAP/52DAP	0.7939	0.803

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.12399	0.089
17DAP/reference	1.15532	0.024
27DAP/reference	1.00061	0.847
39DAP/reference	1.0345	0.615
41DAP/reference	1.18291	0.05
42DAP/reference	1.03211	0.449
43DAP/reference	0.99433	0.861
47DAP/reference	0.96539	0.258
52DAP/reference	0.96437	0.35
57DAP/reference	0.88301	0.014

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.92571	0.509
27DAP/17DAP	0.91843	0.614
39DAP/27DAP	1.11492	0.519
41DAP/39DAP	0.91529	0.465
42DAP/41DAP	1.14097	0.622
43DAP/42DAP	1.08865	0.297
47DAP/43DAP	0.84368	0.075
52DAP/47DAP	1.04745	0.851
57DAP/52DAP	0.95054	0.66
57DAP/7DAP	1.06062	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.8926	0.095
17DAP/reference	0.72278	0.014
27DAP/reference	0.71744	0.01
39DAP/reference	0.85503	0.049
41DAP/reference	0.87383	0.062
42DAP/reference	0.80872	0.034
43DAP/reference	0.82711	0.061
47DAP/reference	0.76867	0.079
52DAP/reference	0.76527	0.012
57DAP/reference	0.69227	0.007

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.23404	0.047
17DAP/reference	1.23738	0.05
27DAP/reference	1.04871	0.961
39DAP/reference	1.20622	0.119
41DAP/reference	0.959	0.277
42DAP/reference	1.01472	1
43DAP/reference	1.07943	0.522
47DAP/reference	0.96968	0.292
52DAP/reference	1.12498	0.061
57DAP/reference	1.30366	0.018

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.89302	0.214
17DAP/reference	0.97705	0.624
27DAP/reference	0.8012	0.046
39DAP/reference	0.72835	0.029
41DAP/reference	0.79724	0.024
42DAP/reference	0.69714	0.023
43DAP/reference	0.70145	0.022
47DAP/reference	0.95706	0.409
52DAP/reference	0.65213	0.072
57DAP/reference	0.5765	0.016

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.97779	1
26DAP/20DAP	0.81534	0.317
34DAP/26DAP	0.99397	1
51DAP/34DAP	0.66976	0.116
52DAP/51DAP	1.15526	0.534
53DAP/52DAP	0.9462	0.79
55DAP/53DAP	1.21288	0.733
57DAP/55DAP	1.03122	0.986
62DAP/57DAP	1.03952	1
68DAP/62DAP	0.70527	0.245
68DAP/14DAP	0.79687	0.375

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.92566	0.285

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	2.54525	0.176
Mature Green Tomato/Ripe Tomato	1.15986	0.715
Immature Eggplant/Mature Eggplant	1.01937	1
Ripe Pepper/Ripe Tomato	0.60625
Mature Eggplant/Ripe Tomato	0.05132

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.00409	1
1-1-2/M82	0.90047	1
12-2/M82	0.89913	0.639
12-4/M82	1.17797	1
1-3/M82	0.52266
2-1-1/M82	1.26564	0.764
2-1/M82	N/A	N/A
2-6/M82	1.16267	0.505
3-2/M82	1.08145
4-1-1/M82	0.76508
4-1/M82	1.20829
4-3-2/M82	N/A	N/A
4-3/M82	0.61674	0.46
5-3/M82	0.8644	0.447
6-2/M82	1.09756
6-3/M82	0.89865	1
7-1/M82	0.71187
7-2/M82	N/A	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	1.02794	0.277
IL2-6/WTpooled	0.85831	0.383
IL7-5/WTpooled	1.34579	0.792
IL7-3/WTpooled	1.01544	1
IL12-4/WTpooled	1.34771	0.523
IL1-4/WTpooled	0.97101	1
WT/WTpooled	1.02492	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	1.01311	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.98199	1
DC3000/delta hrp 6h	1.00125	0.95
DC3000/delta hrp 12h	1.03419	1
DC3000/delta hrp 24h	1.00938	0.84

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	0.83542	1
Exp 36h	0.99021	0.943
Exp 60h	0.90995	0.754

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

hybridization	ratio	FDR (corrected p value)
self-self	0.95668
Var 0h	1.07685	0.936
Var 12h I row2-row1	1.13013	0.283
Var 12h NI row2-row1	0.70272	0.438
Var 36h I row2-row1	0.99537	1
Var 36h NI row2-row1	1.16682	1
Var 60h I row2-row1	0.86732	0.285
Var 60h NI row2-row1	1.30901	0.701
Time course 0hI-0hNI	1.07033	0.799
Time course 12hI-12hNI	1.05315	0.593
Time course 36hI-36hNI	0.94374	0.317
Time course 60hI-60hNI	0.92599	0.319

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)	0.9028	0.33
transgenic ySAMdc/azygous control (breaker)	1.05857	1
transgenic ySAMdc/azygous control (red)	0.98297	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.98153	0.517

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.59417	0.227

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.31766	0.14
Manapal/WT (break)	1.10322	1
Manapal/WT (red)	0.74255	0.229