Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.1.2.9

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.34269	0.656
27DAP/17DAP	1.03272	1
39DAP/27DAP	1.05921	0.876
41DAP/39DAP	1.20071	0.63
42DAP/41DAP	0.9487	1
43DAP/42DAP	1.02114	0.945
47DAP/43DAP	0.74603	0.269
52DAP/47DAP	0.88656	0.693
57DAP/52DAP	1.43481	0.912

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.91975	0.231
17DAP/reference	0.87039	0.043
27DAP/reference	0.97226	0.61
39DAP/reference	1.00083	0.957
41DAP/reference	0.90431	0.201
42DAP/reference	0.86667	0.004
43DAP/reference	0.83717	0.019
47DAP/reference	0.94457	0.161
52DAP/reference	1.21646	0.217
57DAP/reference	1.22212	0.052

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.96883	0.679
27DAP/17DAP	0.90569	0.748
39DAP/27DAP	1.1011	0.793
41DAP/39DAP	0.94834	0.839
42DAP/41DAP	0.9872	0.721
43DAP/42DAP	1.01663	0.585
47DAP/43DAP	0.97505	0.87
52DAP/47DAP	1.10027	0.66
57DAP/52DAP	0.83711	0.321
57DAP/7DAP	1.95314	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.87306	0.203
17DAP/reference	1.11506	0.059
27DAP/reference	1.16839	0.009
39DAP/reference	0.9214	0.039
41DAP/reference	1.05179	0.655
42DAP/reference	1.64187	0.007
43DAP/reference	1.48366	0.011
47DAP/reference	0.97926	0.671
52DAP/reference	1.44774	0.021
57DAP/reference	1.24452	0.029

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.41125	0.17
17DAP/reference	0.93097	0.326
27DAP/reference	1.09042	0.404
39DAP/reference	1.10424	0.164
41DAP/reference	1.19985	0.03
42DAP/reference	1.08589	0.39
43DAP/reference	1.52488	0.327
47DAP/reference	0.88804	0.073
52DAP/reference	1.33711	0.006
57DAP/reference	0.95591	0.433

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.94846	0.391
17DAP/reference	1.12387	0.365
27DAP/reference	1.28092	0.125
39DAP/reference	1.20566	0.043
41DAP/reference	1.28631	0.043
42DAP/reference	1.64758	0.034
43DAP/reference	1.17429	0.426
47DAP/reference	0.99318	0.61
52DAP/reference	0.99825	0.871
57DAP/reference	1.51884	0.008

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.92021	1
26DAP/20DAP	1.23458	0.896
34DAP/26DAP	0.92865	0.826
51DAP/34DAP	1.01419	0.978
52DAP/51DAP	0.99816	1
53DAP/52DAP	2.05439	0.032
55DAP/53DAP	1.09285	0.764
57DAP/55DAP	1.02545	0.845
62DAP/57DAP	0.85684	0.466
68DAP/62DAP	1.55107	0.06
68DAP/14DAP	1.33815	0.236

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.55714	0.028

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	1.747
Immature Eggplant/Mature Eggplant	1.12339	0.554
Ripe Pepper/Ripe Tomato	0.35723	0.293
Mature Eggplant/Ripe Tomato	1.56339	0.373

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	0.76326	0.619
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	0.89267
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	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	0.76602	0.473
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.12484	1
IL12-4/WTpooled	1.18106	0.483
IL1-4/WTpooled	1.0512
WT/WTpooled	0.94587	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	1.04628	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.13728	0.823
DC3000/delta hrp 6h	1.06765	1
DC3000/delta hrp 12h	0.87156	1
DC3000/delta hrp 24h	0.8898	0.654

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	0.80994	1
Exp 36h	1.22946	1
Exp 60h	0.97992	1

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

hybridization	ratio	FDR (corrected p value)
self-self	0.98621	1
Var 0h	0.66001	0.933
Var 12h I row2-row1	1.0758	0.58
Var 12h NI row2-row1	1.33658
Var 36h I row2-row1	1.05884
Var 36h NI row2-row1	N/A	N/A
Var 60h I row2-row1	0.65505
Var 60h NI row2-row1	1.08497	0.157
Time course 0hI-0hNI	0.80959	0.478
Time course 12hI-12hNI	1.08356	0.693
Time course 36hI-36hNI	1.13262	0.453
Time course 60hI-60hNI	0.85986	0.081

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)	1.21842	0.331
transgenic ySAMdc/azygous control (breaker)	1.18393	1
transgenic ySAMdc/azygous control (red)	1.05577	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.00826	0.723

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.09601	1
Manapal/WT (break)	1.61758	0.123
Manapal/WT (red)	1.05826	1