Tomato Functional Genomics Database (TFGD)

Expression of 1-1-8.1.10.15

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.98764	0.801
27DAP/17DAP	1.10179	0.881
39DAP/27DAP	0.82861	0.447
41DAP/39DAP	1.21197	0.676
42DAP/41DAP	1.15944	1
43DAP/42DAP	0.95743	0.906
47DAP/43DAP	1.06238	0.769
52DAP/47DAP	0.95525	0.821
57DAP/52DAP	0.71292	0.687

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.85264	0.07
17DAP/reference	1.20778	0.044
27DAP/reference	0.96382	0.525
39DAP/reference	1.05795	0.639
41DAP/reference	1.20379	0.122
42DAP/reference	1.06721	0.756
43DAP/reference	1.01098	0.942
47DAP/reference	0.89105	0.106
52DAP/reference	0.81096	0.069
57DAP/reference	0.87813	0.074

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.14954	0.525
27DAP/17DAP	0.93379	0.821
39DAP/27DAP	0.98967	0.859
41DAP/39DAP	0.84374	0.093
42DAP/41DAP	1.00316	0.924
43DAP/42DAP	1.03066	0.788
47DAP/43DAP	1.05595	0.772
52DAP/47DAP	1.27661	0.444
57DAP/52DAP	0.97848	0.742
57DAP/7DAP	1.44475	0.365

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.21287	0.15
17DAP/reference	1.45631	0.006
27DAP/reference	1.30687	0.023
39DAP/reference	1.61782	0.005
41DAP/reference	1.5984	0.008
42DAP/reference	1.44576	0.132
43DAP/reference	2.00755	0.006
47DAP/reference	1.19557	0.493
52DAP/reference	1.83599	0.007
57DAP/reference	2.09056	0.003

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.10628	0.443
17DAP/reference	1.07912	0.979
27DAP/reference	0.86773	0.203
39DAP/reference	0.92913	0.221
41DAP/reference	0.91455	0.291
42DAP/reference	0.89403	0.237
43DAP/reference	1.14505	0.874
47DAP/reference	1.06397	0.556
52DAP/reference	0.93683	0.469
57DAP/reference	0.6407	0.107

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.18353	0.069
17DAP/reference	1.12364	0.436
27DAP/reference	1.44108	0.023
39DAP/reference	1.43218	0.02
41DAP/reference	1.41559	0.01
42DAP/reference	1.44146	0.027
43DAP/reference	1.44584	0.092
47DAP/reference	1.03198	0.687
52DAP/reference	1.40162	0.083
57DAP/reference	1.08643	0.892

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.09003	0.966
26DAP/20DAP	1.15864	0.471
34DAP/26DAP	1.02164	1
51DAP/34DAP	1.34773	0.962
52DAP/51DAP	0.92748	1
53DAP/52DAP	1.02153	0.998
55DAP/53DAP	0.985	0.894
57DAP/55DAP	0.4806	0.039
62DAP/57DAP	1.14711	1
68DAP/62DAP	1.05881	1
68DAP/14DAP	0.65608	0.121

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.14847	0.954

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	5.27278	0.058
Mature Green Tomato/Ripe Tomato	0.83113
Immature Eggplant/Mature Eggplant	0.40168
Ripe Pepper/Ripe Tomato	0.17188
Mature Eggplant/Ripe Tomato	1.15561	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.08904	0.877
1-1-2/M82	0.97607	1
12-2/M82	1.01161	1
12-4/M82	0.96771	1
1-3/M82	1.07595	1
2-1-1/M82	1.13981	0.439
2-1/M82	1.08763	1
2-6/M82	1.01029	1
3-2/M82	0.93489
4-1-1/M82	0.90958	1
4-1/M82	0.98563
4-3-2/M82	1.18989
4-3/M82	0.98524	1
5-3/M82	0.99927	1
6-2/M82	1.04982	1
6-3/M82	1.04349	1
7-1/M82	0.97653	0.803
7-2/M82	1.00135	1
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	N/A	N/A
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.7189
IL12-4/WTpooled	N/A	N/A
IL1-4/WTpooled	0.88562
WT/WTpooled	N/A	N/A

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	0.85306	0.75

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.97541	1
DC3000/delta hrp 6h	N/A	N/A
DC3000/delta hrp 12h	0.99064	1
DC3000/delta hrp 24h	1.02914	0.633

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	0.7089

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	N/A	N/A
Exp 36h	N/A	N/A
Exp 60h	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
self-self	0.95967	1
Var 0h	0.87166	1
Var 12h I row2-row1	1.98427	0.58
Var 12h NI row2-row1	1.03958	1
Var 36h I row2-row1	0.99267	1
Var 36h NI row2-row1	0.9747	0.852
Var 60h I row2-row1	0.9895	1
Var 60h NI row2-row1	0.98554	1
Time course 0hI-0hNI	1.10284	0.764
Time course 12hI-12hNI	0.9168	0.119
Time course 36hI-36hNI	0.84708	0.078
Time course 60hI-60hNI	0.51619	0.006

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)	1.67144	0.798
transgenic ySAMdc/azygous control (breaker)	0.89992	1
transgenic ySAMdc/azygous control (red)	1.36329	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.94447	0.128

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.55484	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.88197	1
Manapal/WT (break)	N/A	N/A
Manapal/WT (red)	0.86142	0.181