Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.3.19.20

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.70942	0.206
27DAP/17DAP	1.40883	0.742
39DAP/27DAP	1.01896	0.769
41DAP/39DAP	1.43998	0.338
42DAP/41DAP	1.17641	0.938
43DAP/42DAP	0.89295	0.801
47DAP/43DAP	0.74169	0.274
52DAP/47DAP	2.09051	0.268
57DAP/52DAP	0.68159	0.55

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.85054	0.07
17DAP/reference	0.77782	0.085
27DAP/reference	1.00643	0.904
39DAP/reference	0.78073	0.049
41DAP/reference	0.69129	0.026
42DAP/reference	0.9984	0.469
43DAP/reference	0.98807	0.785
47DAP/reference	1.02683	0.602
52DAP/reference	1.39146	0.008
57DAP/reference	1.17902	0.011

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.82609	0.062
27DAP/17DAP	1.04009	0.988
39DAP/27DAP	1.11369	0.418
41DAP/39DAP	1.2116	0.849
42DAP/41DAP	0.80467	0.125
43DAP/42DAP	1.1348	0.297
47DAP/43DAP	0.94821	0.743
52DAP/47DAP	1.09741	0.66
57DAP/52DAP	1.2026	0.389
57DAP/7DAP	1.19005	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.71692	0.076
17DAP/reference	0.7658	0.011
27DAP/reference	0.74694	0.01
39DAP/reference	0.7313	0.011
41DAP/reference	0.8311	0.039
42DAP/reference	0.85777	0.014
43DAP/reference	0.91472	0.105
47DAP/reference	0.97374	0.671
52DAP/reference	0.78131	0.018
57DAP/reference	0.83686	0.018

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.71812	0.045
17DAP/reference	0.70562	0.009
27DAP/reference	1.0905	0.781
39DAP/reference	1.29043	0.17
41DAP/reference	1.40257	0.007
42DAP/reference	1.26479	0.02
43DAP/reference	0.83753	0.191
47DAP/reference	0.97229	0.459
52DAP/reference	0.9967	0.619
57DAP/reference	0.6206	0.007

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.7979	0.033
17DAP/reference	0.91998	0.47
27DAP/reference	0.89606	0.184
39DAP/reference	0.83834	0.04
41DAP/reference	0.97489	0.56
42DAP/reference	1.28225	0.648
43DAP/reference	1.30968	0.465
47DAP/reference	1.17649	0.847
52DAP/reference	0.76879	0.14
57DAP/reference	2.58765	0.015

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.16681	0.966
26DAP/20DAP	0.98791	1
34DAP/26DAP	1.12068	0.819
51DAP/34DAP	0.84329	0.458
52DAP/51DAP	1.20105	0.606
53DAP/52DAP	1.1488	0.712
55DAP/53DAP	1.02231	0.939
57DAP/55DAP	0.67244	0.109
62DAP/57DAP	1.38195	0.393
68DAP/62DAP	2.69885	0.778
68DAP/14DAP	3.28776	0.022

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.35217	0.092

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.29935	0.019
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	0.19908	0.224
Mature Eggplant/Ripe Tomato	0.06546	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.04412	1
1-1-2/M82	0.8098
12-2/M82	1.29681
12-4/M82	0.99799	1
1-3/M82	0.88082	0.441
2-1-1/M82	1.02865
2-1/M82	N/A	N/A
2-6/M82	1.03328	1
3-2/M82	0.85851
4-1-1/M82	N/A	N/A
4-1/M82	0.95365	1
4-3-2/M82	N/A	N/A
4-3/M82	0.86599	0.611
5-3/M82	0.86578	0.447
6-2/M82	0.99889
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	0.9982	1
9-3-2/M82	0.97923

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.02986
IL2-6/WTpooled	0.92373	1
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.0975	1
IL12-4/WTpooled	0.93509	1
IL1-4/WTpooled	0.93343	0.562
WT/WTpooled	1.09307	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	1.79846

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.06308	0.921
DC3000/delta hrp 6h	N/A	N/A
DC3000/delta hrp 12h	N/A	N/A
DC3000/delta hrp 24h	1.04955	0.779

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	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	1.04689	1
Var 0h	0.73741	0.457
Var 12h I row2-row1	0.95685	0.856
Var 12h NI row2-row1	0.79975	0.488
Var 36h I row2-row1	1.19018	0.742
Var 36h NI row2-row1	0.99278	1
Var 60h I row2-row1	1.11121	0.562
Var 60h NI row2-row1	0.59727	0.977
Time course 0hI-0hNI	1.17532	0.603
Time course 12hI-12hNI	1.0415	0.773
Time course 36hI-36hNI	1.38852	0.039
Time course 60hI-60hNI	1.64005	0.009

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)	1.13435	0.289
transgenic ySAMdc/azygous control (breaker)	0.5843	0.134
transgenic ySAMdc/azygous control (red)	1.12344	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.0303	0.273

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.39369	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.09053	0.105
Manapal/WT (break)	N/A	N/A
Manapal/WT (red)	1.01359	1