Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.3.2.4

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.72137	0.089
27DAP/17DAP	0.83232	0.622
39DAP/27DAP	1.19978	0.84
41DAP/39DAP	0.97931	0.89
42DAP/41DAP	1.3822	0.722
43DAP/42DAP	1.0049	0.914
47DAP/43DAP	0.94819	0.804
52DAP/47DAP	0.92225	0.643
57DAP/52DAP	1.13841	0.977

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.04989	0.662
17DAP/reference	0.84428	0.009
27DAP/reference	0.90756	0.055
39DAP/reference	0.84814	0.017
41DAP/reference	0.80222	0.01
42DAP/reference	0.96103	0.233
43DAP/reference	0.96249	0.48
47DAP/reference	0.99851	0.674
52DAP/reference	1.28251	0.272
57DAP/reference	1.35165	0.022

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.99597	0.782
27DAP/17DAP	1.1618	0.32
39DAP/27DAP	0.87502	0.222
41DAP/39DAP	1.10022	0.497
42DAP/41DAP	1.04481	0.991
43DAP/42DAP	0.83956	0.321
47DAP/43DAP	1.01387	1
52DAP/47DAP	1.03845	0.835
57DAP/52DAP	0.98825	0.841
57DAP/7DAP	0.76707	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.08061	0.393
17DAP/reference	1.17768	0.574
27DAP/reference	1.19585	0.014
39DAP/reference	1.51462	0.04
41DAP/reference	1.21046	0.093
42DAP/reference	1.24174	0.308
43DAP/reference	1.3847	0.167
47DAP/reference	1.1041	0.561
52DAP/reference	1.36947	0.011
57DAP/reference	1.2004	0.007

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.05248	0.484
17DAP/reference	0.97945	0.561
27DAP/reference	1.03381	0.988
39DAP/reference	1.06396	0.935
41DAP/reference	1.12691	0.525
42DAP/reference	1.06959	0.596
43DAP/reference	1.01781	0.787
47DAP/reference	0.85754	0.021
52DAP/reference	1.10711	0.074
57DAP/reference	0.98283	0.581

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.33307	0.207
17DAP/reference	1.14244	0.443
27DAP/reference	1.19292	0.216
39DAP/reference	1.51295	0.02
41DAP/reference	1.4745	0.062
42DAP/reference	1.66311	0.014
43DAP/reference	1.58863	0.016
47DAP/reference	1.05786	1
52DAP/reference	1.45723	0.216
57DAP/reference	1.72747	0.009

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.74972	0.053
26DAP/20DAP	1.39173	0.347
34DAP/26DAP	0.8436	0.879
51DAP/34DAP	1.28468	0.909
52DAP/51DAP	0.94106	1
53DAP/52DAP	1.16342	0.662
55DAP/53DAP	1.48217	0.547
57DAP/55DAP	0.87515	0.527
62DAP/57DAP	0.86535	0.871
68DAP/62DAP	1.25181
68DAP/14DAP	1.51258	0.311

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.39682	0.022

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.08323	1
Mature Green Tomato/Ripe Tomato	3.2097	0.04
Immature Eggplant/Mature Eggplant	0.78143	0.064
Ripe Pepper/Ripe Tomato	5.71003	1
Mature Eggplant/Ripe Tomato	22.0983	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.16771	1
1-1-2/M82	1.48355
12-2/M82	N/A	N/A
12-4/M82	1.44591
1-3/M82	N/A	N/A
2-1-1/M82	0.56571
2-1/M82	N/A	N/A
2-6/M82	0.8546	1
3-2/M82	N/A	N/A
4-1-1/M82	0.83588	1
4-1/M82	1.90247
4-3-2/M82	1.19238	1
4-3/M82	0.85783
5-3/M82	0.90559	1
6-2/M82	0.67304
6-3/M82	0.8667	1
7-1/M82	N/A	N/A
7-2/M82	0.79394	0.381
9-3-2/M82	0.99997

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.89461	0.321
IL2-6/WTpooled	1.14947	1
IL7-5/WTpooled	1.04163	1
IL7-3/WTpooled	0.78623	0.418
IL12-4/WTpooled	0.92472	1
IL1-4/WTpooled	1.09706	1
WT/WTpooled	1.02673	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	1.03861	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.08295	0.894
DC3000/delta hrp 6h	0.98954	0.95
DC3000/delta hrp 12h	0.98127	1
DC3000/delta hrp 24h	0.52406	0.04

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.8556	0.629
DC3000 delta B/DC3000 delta AB	1.08019	0.433

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.89365	0.328
Exp 36h	0.75707	0.504
Exp 60h	0.74227	0.386

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

hybridization	ratio	FDR (corrected p value)
self-self	0.9737	1
Var 0h	1.24423	0.936
Var 12h I row2-row1	1.01578	1
Var 12h NI row2-row1	1.13982	0.649
Var 36h I row2-row1	0.902	1
Var 36h NI row2-row1	1.0684	1
Var 60h I row2-row1	0.74062
Var 60h NI row2-row1	0.91123	0.977
Time course 0hI-0hNI	0.89754	0.347
Time course 12hI-12hNI	1.04575	0.738
Time course 36hI-36hNI	0.9958	0.768
Time course 60hI-60hNI	0.73368	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)	1.0155	0.654
transgenic ySAMdc/azygous control (breaker)	1.1982	0.178
transgenic ySAMdc/azygous control (red)	1.02409	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.99592	0.694

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.29803	0.237

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	2.24291	0.088
Manapal/WT (break)	2.14142	0.123
Manapal/WT (red)	1.41029	0.413