Tomato Functional Genomics Database (TFGD)

Expression of 1-1-5.1.9.13

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.19035	0.63
27DAP/17DAP	1.30583	0.646
39DAP/27DAP	0.78767	0.482
41DAP/39DAP	1.17801	0.545
42DAP/41DAP	1.01035	1
43DAP/42DAP	0.9782	0.925
47DAP/43DAP	1.02467	1
52DAP/47DAP	0.80985	0.54
57DAP/52DAP	0.90903	0.908

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.95788	0.262
17DAP/reference	1.02852	0.399
27DAP/reference	0.98712	0.683
39DAP/reference	1.00832	0.828
41DAP/reference	0.96597	0.434
42DAP/reference	0.93605	0.02
43DAP/reference	0.99957	0.942
47DAP/reference	0.98708	0.445
52DAP/reference	0.86265	0.135
57DAP/reference	0.95711	0.308

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.97352	0.629
27DAP/17DAP	1.03426	0.923
39DAP/27DAP	0.98404	0.775
41DAP/39DAP	1.03701	0.781
42DAP/41DAP	0.97387	0.751
43DAP/42DAP	0.99791	1
47DAP/43DAP	0.96726	0.734
52DAP/47DAP	0.99621	0.975
57DAP/52DAP	1.01826	0.906
57DAP/7DAP	1.00299	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.87634	0.072
17DAP/reference	0.78403	0.011
27DAP/reference	0.84869	0.028
39DAP/reference	0.74323	0.011
41DAP/reference	0.73823	0.031
42DAP/reference	0.76019	0.01
43DAP/reference	0.77023	0.018
47DAP/reference	0.81485	0.101
52DAP/reference	0.74394	0.017
57DAP/reference	0.73929	0.007

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.07979	0.35
17DAP/reference	1.04839	0.406
27DAP/reference	0.92302	0.144
39DAP/reference	0.94678	0.173
41DAP/reference	0.90486	0.068
42DAP/reference	0.88108	0.024
43DAP/reference	1.1065	0.338
47DAP/reference	0.91432	0.053
52DAP/reference	1.01936	0.417
57DAP/reference	1.09832	0.026

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.83227	0.034
17DAP/reference	0.918	0.262
27DAP/reference	0.74391	0.044
39DAP/reference	0.72688	0.01
41DAP/reference	0.83648	0.019
42DAP/reference	0.78988	0.02
43DAP/reference	0.79898	0.017
47DAP/reference	0.92439	0.168
52DAP/reference	0.94924	0.623
57DAP/reference	0.74115	0.021

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.9848	1
26DAP/20DAP	1.01947	1
34DAP/26DAP	1.02804	1
51DAP/34DAP	0.99241	0.927
52DAP/51DAP	0.97998	1
53DAP/52DAP	1.15303	0.24
55DAP/53DAP	1.0435	0.955
57DAP/55DAP	0.96666	0.845
62DAP/57DAP	1.07041	0.833
68DAP/62DAP	1.07859	0.792
68DAP/14DAP	1.07971	0.785

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.9338	0.108

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.70398	0.23
Mature Green Tomato/Ripe Tomato	1.72242	0.017
Immature Eggplant/Mature Eggplant	0.93428	0.72
Ripe Pepper/Ripe Tomato	1.68098	1
Mature Eggplant/Ripe Tomato	1.86765	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.0444	1
1-1-2/M82	0.91057	1
12-2/M82	1.06384	1
12-4/M82	0.95051	1
1-3/M82	N/A	N/A
2-1-1/M82	1.03602	0.764
2-1/M82	1.17232	0.312
2-6/M82	0.96474	1
3-2/M82	0.96762
4-1-1/M82	0.95599	0.962
4-1/M82	0.99423
4-3-2/M82	1.05667	0.232
4-3/M82	1.04066	1
5-3/M82	1.00065	1
6-2/M82	0.99701	1
6-3/M82	1.05732	1
7-1/M82	0.89806
7-2/M82	0.98598	1
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.03954	1
IL2-6/WTpooled	0.91797	1
IL7-5/WTpooled	1.24894	0.75
IL7-3/WTpooled	1.11764	1
IL12-4/WTpooled	1.07076	0.891
IL1-4/WTpooled	0.90929	1
WT/WTpooled	0.97744	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	0.89039	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.93259	1
DC3000/delta hrp 6h	1.03603	0.95
DC3000/delta hrp 12h	0.95617	1
DC3000/delta hrp 24h	1.04528	0.71

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.94398	0.485
DC3000 delta B/DC3000 delta AB	1.02977	0.565

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.12506	1
Exp 36h	1.12527	0.489
Exp 60h	1.32856	0.563

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

hybridization	ratio	FDR (corrected p value)
self-self	1.02672	1
Var 0h	0.8727	1
Var 12h I row2-row1	1.09839	0.209
Var 12h NI row2-row1	1.13198	1
Var 36h I row2-row1	1.03023	1
Var 36h NI row2-row1	0.92645	0.584
Var 60h I row2-row1	1.10214	0.562
Var 60h NI row2-row1	1.12895	0.904
Time course 0hI-0hNI	1.05567	0.867
Time course 12hI-12hNI	1.02504	0.867
Time course 36hI-36hNI	1.07677	0.248
Time course 60hI-60hNI	1.07294	0.216

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)	1.00307	0.921
transgenic ySAMdc/azygous control (breaker)	1.29785	0.178
transgenic ySAMdc/azygous control (red)	1.06496	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.98717	0.431

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.01447	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.12237	1
Manapal/WT (break)	1.26903	0.381
Manapal/WT (red)	1.05998	1