Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.3.6.8

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.93712	0.64
27DAP/17DAP	1.05912	0.92
39DAP/27DAP	0.85421	0.549
41DAP/39DAP	1.22243	0.483
42DAP/41DAP	0.76963	1
43DAP/42DAP	0.97662	0.918
47DAP/43DAP	1.09491	0.618
52DAP/47DAP	1.47882	0.303
57DAP/52DAP	1.24218	0.988

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.71921	0.098
17DAP/reference	0.7814	0.024
27DAP/reference	0.86645	0.073
39DAP/reference	0.79703	0.083
41DAP/reference	0.85202	0.114
42DAP/reference	1.39911	0.001
43DAP/reference	1.21849	0.009
47DAP/reference	0.95891	0.258
52DAP/reference	0.78128	0.044
57DAP/reference	1.03616	0.802

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.99718	0.782
27DAP/17DAP	0.97357	0.943
39DAP/27DAP	0.8606	0.377
41DAP/39DAP	0.93184	0.696
42DAP/41DAP	0.95854	0.708
43DAP/42DAP	1.18657	0.351
47DAP/43DAP	0.89962	0.534
52DAP/47DAP	0.92913	0.807
57DAP/52DAP	1.17519	0.344
57DAP/7DAP	1.69216	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.13173	0.534
17DAP/reference	1.21599	0.042
27DAP/reference	1.24035	0.131
39DAP/reference	0.99412	0.745
41DAP/reference	1.03307	0.836
42DAP/reference	1.00067	0.675
43DAP/reference	1.06646	0.537
47DAP/reference	1.05459	1
52DAP/reference	1.33328	0.025
57DAP/reference	1.11296	0.232

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.84891	0.204
17DAP/reference	0.81708	0.075
27DAP/reference	0.86005	0.081
39DAP/reference	0.83581	0.085
41DAP/reference	1.01364	1
42DAP/reference	0.76248	0.028
43DAP/reference	0.90788	0.212
47DAP/reference	0.86466	0.027
52DAP/reference	0.79297	0.02
57DAP/reference	0.89973	0.092

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.06826	0.74
17DAP/reference	1.03688	0.855
27DAP/reference	1.22784	0.227
39DAP/reference	1.07763	0.912
41DAP/reference	1.24343	0.156
42DAP/reference	1.13925	0.226
43DAP/reference	1.20812	0.1
47DAP/reference	1.26058	0.034
52DAP/reference	1.33973	0.592
57DAP/reference	0.85962	0.158

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.1665	0.966
26DAP/20DAP	0.75919	0.512
34DAP/26DAP	0.59601	0.548
51DAP/34DAP	0.94828	0.722
52DAP/51DAP	1.0871	0.733
53DAP/52DAP	1.10773	0.565
55DAP/53DAP	1.28253	0.511
57DAP/55DAP	1.30284	0.793
62DAP/57DAP	1.07684	0.902
68DAP/62DAP	0.98307	0.885
68DAP/14DAP	1.0922	0.656

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	2.6979	0.099

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	3.34962
Mature Green Tomato/Ripe Tomato	0.77126	0.256
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	N/A	N/A
Mature Eggplant/Ripe Tomato	1.86204

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.186	0.877
1-1-2/M82	1.0368
12-2/M82	N/A	N/A
12-4/M82	1.35175
1-3/M82	0.4558
2-1-1/M82	N/A	N/A
2-1/M82	1.2878
2-6/M82	0.96226	1
3-2/M82	N/A	N/A
4-1-1/M82	N/A	N/A
4-1/M82	1.40535
4-3-2/M82	N/A	N/A
4-3/M82	N/A	N/A
5-3/M82	0.89989	1
6-2/M82	N/A	N/A
6-3/M82	1.01876
7-1/M82	N/A	N/A
7-2/M82	0.78193	0.414
9-3-2/M82	1.33962

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.08545
IL2-6/WTpooled	1.03895	1
IL7-5/WTpooled	0.53624	1
IL7-3/WTpooled	0.9165	1
IL12-4/WTpooled	0.72159	0.543
IL1-4/WTpooled	1.04492	1
WT/WTpooled	1.05669	0.85

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	1.09811	0.222

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.89412	0.807
DC3000/delta hrp 6h	1.29089	1
DC3000/delta hrp 12h	1.02062	1
DC3000/delta hrp 24h	1.07056	0.483

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.13111
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	0.50073	1
Exp 36h	0.81424	0.406
Exp 60h	0.91314	0.522

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

hybridization	ratio	FDR (corrected p value)
self-self	1.08214	1
Var 0h	1.06223	0.98
Var 12h I row2-row1	1.11359	0.58
Var 12h NI row2-row1	0.99793	1
Var 36h I row2-row1	0.92722	1
Var 36h NI row2-row1	1.02339	1
Var 60h I row2-row1	1.0267	1
Var 60h NI row2-row1	0.9896	1
Time course 0hI-0hNI	0.98649	0.95
Time course 12hI-12hNI	1.05926	0.82
Time course 36hI-36hNI	1.10381	0.07
Time course 60hI-60hNI	1.27064	0.012

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)	2.75427	1
transgenic ySAMdc/azygous control (breaker)	2.78245	0.172
transgenic ySAMdc/azygous control (red)	1.27816	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.94512	0.149

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.01266	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	N/A	N/A
Manapal/WT (break)	1.05857	1
Manapal/WT (red)	1.59691	0.137