Tomato Functional Genomics Database (TFGD)

Expression of 1-1-8.3.9.20

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.3637	0.219
27DAP/17DAP	1.00265	0.885
39DAP/27DAP	2.02567	0.601
41DAP/39DAP	1.04938	0.735
42DAP/41DAP	1.12022	0.978
43DAP/42DAP	0.85097	0.71
47DAP/43DAP	1.1953	0.825
52DAP/47DAP	0.77268	0.554
57DAP/52DAP	1.33784	0.694

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.92973	0.326
17DAP/reference	1.05329	0.606
27DAP/reference	1.06486	0.415
39DAP/reference	1.02298	0.828
41DAP/reference	1.03469	0.855
42DAP/reference	0.78607	0.013
43DAP/reference	1.01929	0.942
47DAP/reference	0.83497	0.021
52DAP/reference	0.89799	0.215
57DAP/reference	0.89209	0.294

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.33845	0.23
27DAP/17DAP	1.15251	0.557
39DAP/27DAP	1.0243	0.698
41DAP/39DAP	1.1649	0.774
42DAP/41DAP	0.9081	0.572
43DAP/42DAP	1.08322	0.585
47DAP/43DAP	0.95575	0.846
52DAP/47DAP	0.92683	0.777
57DAP/52DAP	0.88914	0.422
57DAP/7DAP	1.33752	0.365

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.8073	0.129
17DAP/reference	0.94811	0.338
27DAP/reference	1.1899	0.131
39DAP/reference	0.84708	0.17
41DAP/reference	0.92054	0.271
42DAP/reference	0.86761	0.178
43DAP/reference	1.10306	0.923
47DAP/reference	1.07205	0.745
52DAP/reference	0.87939	0.072
57DAP/reference	0.92206	0.328

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.20587	0.116
17DAP/reference	1.00231	0.711
27DAP/reference	0.90177	0.22
39DAP/reference	0.8694	0.227
41DAP/reference	0.80987	0.118
42DAP/reference	0.78771	0.067
43DAP/reference	1.29973	0.188
47DAP/reference	0.9767	0.5
52DAP/reference	1.01257	1
57DAP/reference	0.85914	0.259

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.98459	0.607
17DAP/reference	1.08499	0.775
27DAP/reference	1.17547	0.092
39DAP/reference	1.04851	0.578
41DAP/reference	0.94701	0.459
42DAP/reference	0.99041	0.816
43DAP/reference	0.95488	0.468
47DAP/reference	1.02056	0.754
52DAP/reference	1.94761	0.639
57DAP/reference	0.72319	0.054

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.9361	1
26DAP/20DAP	0.94779	1
34DAP/26DAP	1.08947	0.819
51DAP/34DAP	1.00694	1
52DAP/51DAP	0.98398	1
53DAP/52DAP	1.19945	0.413
55DAP/53DAP	1.3858	0.562
57DAP/55DAP	1.25505	0.71
62DAP/57DAP	1.04072	0.994
68DAP/62DAP	0.9649	0.787
68DAP/14DAP	0.82719	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.82285	0.166

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	2.54727
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	1.34342
Mature Eggplant/Ripe Tomato	1.064

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.85808	0.934
1-1-2/M82	1.09221
12-2/M82	N/A	N/A
12-4/M82	0.94754
1-3/M82	N/A	N/A
2-1-1/M82	0.62506
2-1/M82	N/A	N/A
2-6/M82	N/A	N/A
3-2/M82	N/A	N/A
4-1-1/M82	N/A	N/A
4-1/M82	N/A	N/A
4-3-2/M82	N/A	N/A
4-3/M82	0.97517
5-3/M82	1.18486	1
6-2/M82	N/A	N/A
6-3/M82	1.03597
7-1/M82	N/A	N/A
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	N/A	N/A
IL2-6/WTpooled	1.48867	0.584
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.98474	1
IL12-4/WTpooled	1.00899	0.839
IL1-4/WTpooled	1.0649
WT/WTpooled	1.09319	0.89

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	0.7985	0.497

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.94761	1
DC3000/delta hrp 6h	N/A	N/A
DC3000/delta hrp 12h	0.95487	1
DC3000/delta hrp 24h	0.85555	0.17

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	0.88559	1
Exp 36h	1.35006	1
Exp 60h	1.20325	1

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

hybridization	ratio	FDR (corrected p value)
self-self	1.19273	1
Var 0h	1.69827	0.421
Var 12h I row2-row1	1.05117	1
Var 12h NI row2-row1	0.95128	0.906
Var 36h I row2-row1	1.1715	1
Var 36h NI row2-row1	0.91528	0.791
Var 60h I row2-row1	0.98359
Var 60h NI row2-row1	1.07878	0.904
Time course 0hI-0hNI	0.97785	0.922
Time course 12hI-12hNI	1.03262	0.803
Time course 36hI-36hNI	0.97988	0.549
Time course 60hI-60hNI	1.00367	1

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)	1.03593	0.321
transgenic ySAMdc/azygous control (breaker)	1.01957	1
transgenic ySAMdc/azygous control (red)	0.94354	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.00976	0.619

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.86531	0.284

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.72948	1
Manapal/WT (break)	0.66693	0.333
Manapal/WT (red)	0.63437	0.181