Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.4.16.21

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.17253	0.67
27DAP/17DAP	1.20763	0.88
39DAP/27DAP	1.45353	0.184
41DAP/39DAP	0.89472	0.645
42DAP/41DAP	1.25938	0.802
43DAP/42DAP	0.89014	0.829
47DAP/43DAP	1.30892	0.595
52DAP/47DAP	1.09481	0.976
57DAP/52DAP	0.96709	0.957

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.75673	0.027
17DAP/reference	0.90278	0.079
27DAP/reference	0.93902	0.359
39DAP/reference	0.9938	0.901
41DAP/reference	0.91895	0.201
42DAP/reference	1.01781	0.656
43DAP/reference	1.18149	0.022
47DAP/reference	1.30827	0.002
52DAP/reference	1.3545	0.02
57DAP/reference	1.21368	0.027

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.86192	0.311
27DAP/17DAP	1.15343	0.671
39DAP/27DAP	1.45562	0.174
41DAP/39DAP	0.80452	0.038
42DAP/41DAP	1.12657	0.8
43DAP/42DAP	1.20928	0.273
47DAP/43DAP	1.21277	0.827
52DAP/47DAP	1.08891	0.779
57DAP/52DAP	0.68718	0.068
57DAP/7DAP	1.24984	0.365

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.81716	0.086
17DAP/reference	0.75907	0.024
27DAP/reference	1.03543	0.974
39DAP/reference	0.91546	0.198
41DAP/reference	1.01763	0.891
42DAP/reference	0.88862	0.042
43DAP/reference	1.10196	0.289
47DAP/reference	1.12207	0.266
52DAP/reference	1.00537	0.802
57DAP/reference	0.91063	0.097

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.80784	0.011
17DAP/reference	0.80325	0.023
27DAP/reference	0.86498	0.079
39DAP/reference	0.91738	0.129
41DAP/reference	0.9313	0.212
42DAP/reference	0.93569	0.15
43DAP/reference	1.03684	1
47DAP/reference	0.98971	0.609
52DAP/reference	0.94705	0.203
57DAP/reference	0.84972	0.01

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.84776	0.127
17DAP/reference	1.69067	0.746
27DAP/reference	0.9441	0.397
39DAP/reference	0.96982	0.504
41DAP/reference	0.9434	0.417
42DAP/reference	0.90958	0.287
43DAP/reference	1.05872	0.755
47DAP/reference	1.17606	0.053
52DAP/reference	1.08193	0.965
57DAP/reference	1.15895	0.074

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.35107	0.966
26DAP/20DAP	1.0739	0.905
34DAP/26DAP	1.02866	1
51DAP/34DAP	0.95888	0.737
52DAP/51DAP	1.18678	0.842
53DAP/52DAP	1.16111	0.712
55DAP/53DAP	1.27154	0.266
57DAP/55DAP	1.06206	1
62DAP/57DAP	1.14328	0.902
68DAP/62DAP	1.0736	0.914
68DAP/14DAP	1.18727	0.656

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	2.53926	0.021

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.61391	0.027
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	0.15226	0.224
Mature Eggplant/Ripe Tomato	0.11048	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.28058	0.742
1-1-2/M82	1.16782	1
12-2/M82	1.12741	1
12-4/M82	1.00038
1-3/M82	2.15267	0.26
2-1-1/M82	1.36173	0.375
2-1/M82	1.09529	1
2-6/M82	1.04546	1
3-2/M82	1.53924	0.717
4-1-1/M82	1.04299	1
4-1/M82	0.60723
4-3-2/M82	0.94172	0.37
4-3/M82	1.2823	1
5-3/M82	0.92105	1
6-2/M82	1.11839	1
6-3/M82	0.85555	1
7-1/M82	0.7051	0.408
7-2/M82	1.27527	0.318
9-3-2/M82	0.98405	0.449

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.27365	0.277
IL2-6/WTpooled	0.66681	0.473
IL7-5/WTpooled	0.99641	1
IL7-3/WTpooled	1.60755	1
IL12-4/WTpooled	1.19987	1
IL1-4/WTpooled	1.09548	1
WT/WTpooled	0.94814	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	0.39917

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.02306	0.921
DC3000/delta hrp 6h	N/A	N/A
DC3000/delta hrp 12h	1.0207	1
DC3000/delta hrp 24h	1.20073	0.069

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	1.56474	0.177

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.24504	1
Exp 36h	1.36546	0.693
Exp 60h	1.6105	0.221

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

hybridization	ratio	FDR (corrected p value)
self-self	1.04407	1
Var 0h	0.6297	1
Var 12h I row2-row1	0.89921	0.77
Var 12h NI row2-row1	0.75349	0.488
Var 36h I row2-row1	1.18755
Var 36h NI row2-row1	1.24399	1
Var 60h I row2-row1	0.95778	0.582
Var 60h NI row2-row1	1.22317	1
Time course 0hI-0hNI	1.40805	0.833
Time course 12hI-12hNI	0.88081	0.522
Time course 36hI-36hNI	0.98052	0.589
Time course 60hI-60hNI	0.90029	0.646

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)	0.60887	0.299
transgenic ySAMdc/azygous control (breaker)	2.7116	0.166
transgenic ySAMdc/azygous control (red)	1.33724	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.10986	0.035

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.98142	0.789

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	3.1606	0.105
Manapal/WT (break)	1.03976	1
Manapal/WT (red)	0.77321	0.242