Tomato Functional Genomics Database (TFGD)

Expression of 1-1-5.4.5.7

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.57647	0.098
27DAP/17DAP	0.95557	0.964
39DAP/27DAP	1.08591	0.87
41DAP/39DAP	0.85744	0.636
42DAP/41DAP	1.00786	1
43DAP/42DAP	1.01764	0.93
47DAP/43DAP	0.98109	0.835
52DAP/47DAP	1.01205	0.916
57DAP/52DAP	1.79333	0.964

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.75337	0.03
17DAP/reference	0.82533	0.016
27DAP/reference	0.89809	0.089
39DAP/reference	0.94312	0.404
41DAP/reference	0.79717	0.049
42DAP/reference	0.80217	0.003
43DAP/reference	0.92819	0.259
47DAP/reference	0.84343	0.018
52DAP/reference	0.92193	0.147
57DAP/reference	1.1471	0.195

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.80805	0.245
27DAP/17DAP	1.15492	0.719
39DAP/27DAP	0.99145	0.87
41DAP/39DAP	0.94974	0.923
42DAP/41DAP	0.96647	0.721
43DAP/42DAP	1.26837	0.192
47DAP/43DAP	1.00147	1
52DAP/47DAP	1.15196	0.552
57DAP/52DAP	1.08396	0.659
57DAP/7DAP	0.81804	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.88841	0.058
17DAP/reference	0.82636	0.011
27DAP/reference	0.83931	0.01
39DAP/reference	0.9305	0.109
41DAP/reference	0.80948	0.021
42DAP/reference	0.7501	0.01
43DAP/reference	0.83014	0.049
47DAP/reference	0.8179	0.168
52DAP/reference	0.86147	0.028
57DAP/reference	0.75531	0.006

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.85849	0.11
17DAP/reference	0.75245	0.021
27DAP/reference	0.89941	0.24
39DAP/reference	0.96081	0.428
41DAP/reference	0.95546	0.348
42DAP/reference	0.7812	0.022
43DAP/reference	0.85236	0.084
47DAP/reference	0.9177	0.159
52DAP/reference	0.95836	0.407
57DAP/reference	0.75393	0.003

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.82397	0.087
17DAP/reference	0.94292	0.452
27DAP/reference	0.84823	0.031
39DAP/reference	0.83352	0.037
41DAP/reference	0.85688	0.02
42DAP/reference	0.76487	0.016
43DAP/reference	0.90758	0.068
47DAP/reference	0.90236	0.207
52DAP/reference	1.05154	0.69
57DAP/reference	0.96727	0.509

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.08685	0.966
26DAP/20DAP	0.98563	1
34DAP/26DAP	1.16639	1
51DAP/34DAP	0.8245	0.078
52DAP/51DAP	0.95302	1
53DAP/52DAP	1.55242	0.858
55DAP/53DAP	1.16349	0.981
57DAP/55DAP	0.82809	0.337
62DAP/57DAP	1.29628	0.115
68DAP/62DAP	1.43719	0.089
68DAP/14DAP	0.91674	0.121

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.90786	0.304

Experiment: Solanaceae fruit comparison

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

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	N/A	N/A
12-2/M82	N/A	N/A
12-4/M82	N/A	N/A
1-3/M82	N/A	N/A
2-1-1/M82	N/A	N/A
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	N/A	N/A
5-3/M82	N/A	N/A
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	N/A	N/A
9-3-2/M82	0.89671

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.86926	1
IL2-6/WTpooled	0.49266	1
IL7-5/WTpooled	0.55959
IL7-3/WTpooled	0.65556	0.298
IL12-4/WTpooled	0.95062	1
IL1-4/WTpooled	0.7165	0.834
WT/WTpooled	0.99563	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	1.30617	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.19024	0.894
DC3000/delta hrp 6h	1.20762	0.777
DC3000/delta hrp 12h	1.15764	1
DC3000/delta hrp 24h	0.67923	0.035

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.90373	0.803
DC3000 delta B/DC3000 delta AB	0.94828	0.619

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.18207	1
Exp 36h	0.85961	0.661
Exp 60h	0.84107	0.664

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

hybridization	ratio	FDR (corrected p value)
self-self	1.02451	1
Var 0h	N/A	N/A
Var 12h I row2-row1	0.95464	0.856
Var 12h NI row2-row1	1.10525	0.649
Var 36h I row2-row1	0.92736	1
Var 36h NI row2-row1	1.355	0.482
Var 60h I row2-row1	1.07131	1
Var 60h NI row2-row1	1.1151	1
Time course 0hI-0hNI	1.06602	0.799
Time course 12hI-12hNI	0.91299	0.295
Time course 36hI-36hNI	0.84514	0.144
Time course 60hI-60hNI	0.26834	0.005

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)	274.619	0.431
transgenic ySAMdc/azygous control (breaker)	3.4958	0.248
transgenic ySAMdc/azygous control (red)	1.7205	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.94785	0.055

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.45364	0.231

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.05966	0.307
Manapal/WT (break)	0.92406	1
Manapal/WT (red)	0.98008	0.503