Tomato Functional Genomics Database (TFGD)

Expression of 1-1-8.1.6.11

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.85119	0.347
27DAP/17DAP	0.90312	0.783
39DAP/27DAP	1.20128	0.732
41DAP/39DAP	1.55358	0.153
42DAP/41DAP	1.34648	0.644
43DAP/42DAP	1.57575	0.23
47DAP/43DAP	1.49879	0.316
52DAP/47DAP	0.71622	0.331
57DAP/52DAP	0.90562	0.94

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.58984	0.054
17DAP/reference	0.59545	0.015
27DAP/reference	0.67872	0.043
39DAP/reference	1.10777	0.654
41DAP/reference	0.69729	0.039
42DAP/reference	1.62545	0.001
43DAP/reference	4.89117	0.006
47DAP/reference	2.558	0.001
52DAP/reference	1.33125	0.092
57DAP/reference	2.61715	0.02

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.84964	0.402
27DAP/17DAP	1.08833	1
39DAP/27DAP	1.11845	0.553
41DAP/39DAP	1.00428	0.986
42DAP/41DAP	1.21711	0.763
43DAP/42DAP	0.8503	0.246
47DAP/43DAP	1.078	0.735
52DAP/47DAP	1.0449	0.93
57DAP/52DAP	0.94769	0.7
57DAP/7DAP	0.81215	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.87611	0.361
17DAP/reference	1.18983	0.361
27DAP/reference	0.91969	0.402
39DAP/reference	0.94411	0.411
41DAP/reference	0.80866	0.116
42DAP/reference	0.76741	0.034
43DAP/reference	1.10831	0.707
47DAP/reference	1.2888	0.43
52DAP/reference	1.08733	0.781
57DAP/reference	1.14643	0.41

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.60087	0.009
17DAP/reference	0.54567	0.004
27DAP/reference	0.62399	0.012
39DAP/reference	0.52687	0.012
41DAP/reference	0.66922	0.01
42DAP/reference	1.4677	0.68
43DAP/reference	0.75468	0.013
47DAP/reference	1.04216	0.812
52DAP/reference	0.69381	0.072
57DAP/reference	0.64309	0.006

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.73931	0.147
17DAP/reference	0.46568	0.002
27DAP/reference	0.58266	0.085
39DAP/reference	0.67086	0.022
41DAP/reference	0.85462
42DAP/reference	1.44711	0.529
43DAP/reference	1.69806	0.107
47DAP/reference	2.75384	0.005
52DAP/reference	2.05207	0.252
57DAP/reference	0.96999	0.5

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.30364	0.966
26DAP/20DAP	1.06716	1
34DAP/26DAP	0.74313	0.653
51DAP/34DAP	1.66396	0.677
52DAP/51DAP	1.08321
53DAP/52DAP	0.95277	0.876
55DAP/53DAP	1.25591	0.184
57DAP/55DAP	0.90992	0.731
62DAP/57DAP	N/A	N/A
68DAP/62DAP	0.77928	0.263
68DAP/14DAP	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.0692	0.954

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	62.9279	0.058
Mature Green Tomato/Ripe Tomato	0.66555	0.047
Immature Eggplant/Mature Eggplant	0.35348	0.062
Ripe Pepper/Ripe Tomato	0.03802	0.224
Mature Eggplant/Ripe Tomato	0.49845	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	1.66243	1
12-2/M82	0.69601
12-4/M82	1.40225	1
1-3/M82	N/A	N/A
2-1-1/M82	1.00489	1
2-1/M82	0.62943
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	0.75898
4-3-2/M82	2.0562	0.241
4-3/M82	1.5535	0.268
5-3/M82	1.00689	1
6-2/M82	1.82305	0.212
6-3/M82	0.75724	0.232
7-1/M82	1.08486	1
7-2/M82	0.61118
9-3-2/M82	1.69305	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.62116	0.243
IL2-6/WTpooled	0.41443	0.348
IL7-5/WTpooled	1.1127	0.635
IL7-3/WTpooled	1.15461	1
IL12-4/WTpooled	0.94958	1
IL1-4/WTpooled	0.80538	0.476
WT/WTpooled	0.91335	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	0.83055	0.75

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.61956
DC3000/delta hrp 6h	0.59294	0.613
DC3000/delta hrp 12h	1.04648	1
DC3000/delta hrp 24h	1.78135	0.165

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	N/A	N/A
Exp 36h	0.96212	1
Exp 60h	0.77242	0.386

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

hybridization	ratio	FDR (corrected p value)
self-self	0.97137	1
Var 0h	0.62819	0.933
Var 12h I row2-row1	0.87239
Var 12h NI row2-row1	0.77878
Var 36h I row2-row1	0.93716
Var 36h NI row2-row1	0.73914
Var 60h I row2-row1	0.91406	0.952
Var 60h NI row2-row1	1.22817
Time course 0hI-0hNI	0.97797	0.936
Time course 12hI-12hNI	0.9615	0.752
Time course 36hI-36hNI	0.88173	0.265
Time course 60hI-60hNI	0.75559	0.007

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)	0.62171	0.324
transgenic ySAMdc/azygous control (breaker)	1.07553	0.248
transgenic ySAMdc/azygous control (red)	0.93432	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.0261	0.619

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.70735	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	2.07161	0.09
Manapal/WT (break)	1.10149	0.381
Manapal/WT (red)	0.72034	0.181