Tomato Functional Genomics Database (TFGD)

Expression of 1-1-6.2.10.12

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.25367	0.477
27DAP/17DAP	0.76167	0.324
39DAP/27DAP	1.25202	0.463
41DAP/39DAP	0.82997	0.373
42DAP/41DAP	1.18114	0.888
43DAP/42DAP	1.44028	0.507
47DAP/43DAP	1.04871	0.876
52DAP/47DAP	0.868	0.63
57DAP/52DAP	1.04418	0.983

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.22134	0.047
17DAP/reference	1.02335	0.787
27DAP/reference	1.14052	0.782
39DAP/reference	0.94116	0.412
41DAP/reference	0.8777	0.341
42DAP/reference	1.16231	0.191
43DAP/reference	1.44003	0.017
47DAP/reference	1.39738	0.007
52DAP/reference	1.24635	0.041
57DAP/reference	1.16417	0.166

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.00885	0.826
27DAP/17DAP	1.15585	0.55
39DAP/27DAP	0.90221	0.291
41DAP/39DAP	1.0929	0.914
42DAP/41DAP	1.0233	1
43DAP/42DAP	1.37923	0.038
47DAP/43DAP	1.09675	0.681
52DAP/47DAP	0.79222	0.255
57DAP/52DAP	0.87355	0.17
57DAP/7DAP	1.51394	0.365

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.54367	0.037
17DAP/reference	1.94347	0.006
27DAP/reference	1.97389	0.007
39DAP/reference	2.42596	0.005
41DAP/reference	2.51766	0.011
42DAP/reference	2.59102	0.006
43DAP/reference	2.96215	0.006
47DAP/reference	2.00734	0.022
52DAP/reference	2.20936	0.009
57DAP/reference	1.38456	0.04

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.455	0.226
17DAP/reference	1.21402	0.229
27DAP/reference	1.2847	0.066
39DAP/reference	1.06615	1
41DAP/reference	0.99264	0.545
42DAP/reference	1.14998	0.121
43DAP/reference	0.88781	0.292
47DAP/reference	1.09625	0.467
52DAP/reference	0.94632	0.433
57DAP/reference	0.91173	0.298

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.55173	0.015
17DAP/reference	1.35915	0.151
27DAP/reference	1.66353	0.021
39DAP/reference	1.81302	0.012
41DAP/reference	1.74101	0.012
42DAP/reference	1.85725	0.007
43DAP/reference	1.95057	0.008
47DAP/reference	1.66222	0.006
52DAP/reference	2.08821	0.035
57DAP/reference	1.67139	0.079

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	3.05526	0.966
26DAP/20DAP	1.21733	0.785
34DAP/26DAP	0.90584	0.753
51DAP/34DAP	1.05485	0.869
52DAP/51DAP	0.65193	0.151
53DAP/52DAP	1.30803	0.221
55DAP/53DAP	1.19589	0.771
57DAP/55DAP	1.13638	0.898
62DAP/57DAP	0.57849	0.162
68DAP/62DAP	1.60005	0.597
68DAP/14DAP	1.57887

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.78317	0.198

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.82458	0.279
Mature Green Tomato/Ripe Tomato	1.00362	0.774
Immature Eggplant/Mature Eggplant	0.67053	0.062
Ripe Pepper/Ripe Tomato	2.12845	0.258
Mature Eggplant/Ripe Tomato	1.31724	0.373

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.27254	0.742
1-1-2/M82	1.33205	1
12-2/M82	0.85271	0.74
12-4/M82	1.08542	1
1-3/M82	3.56307	0.248
2-1-1/M82	0.96927
2-1/M82	0.71262
2-6/M82	1.05704	1
3-2/M82	1.71221
4-1-1/M82	1.26829	1
4-1/M82	N/A	N/A
4-3-2/M82	2.15762
4-3/M82	2.02405	0.268
5-3/M82	0.74395	0.642
6-2/M82	2.16316
6-3/M82	1.26394	1
7-1/M82	1.2517
7-2/M82	N/A	N/A
9-3-2/M82	1.87772

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	1.00557	1
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.0332	1
IL12-4/WTpooled	0.95832	1
IL1-4/WTpooled	0.8981	1
WT/WTpooled	1.06987	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	1.19563	0.309

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.04987	0.921
DC3000/delta hrp 6h	0.88359	0.95
DC3000/delta hrp 12h	0.97657	1
DC3000/delta hrp 24h	1.08129	0.62

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	1.11202	0.528

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	N/A	N/A
Exp 36h	0.95458	0.879
Exp 60h	1.26399	0.563

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

hybridization	ratio	FDR (corrected p value)
self-self	1.02599	1
Var 0h	0.92809	1
Var 12h I row2-row1	0.82285	0.654
Var 12h NI row2-row1	0.99053	0.906
Var 36h I row2-row1	1.36565	0.742
Var 36h NI row2-row1	0.66862	0.61
Var 60h I row2-row1	0.9396	0.306
Var 60h NI row2-row1	0.89845	0.516
Time course 0hI-0hNI	1.20921	0.574
Time course 12hI-12hNI	1.00458	1
Time course 36hI-36hNI	1.13866	0.039
Time course 60hI-60hNI	1.5473	0.008

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)	0.88386	0.254
transgenic ySAMdc/azygous control (breaker)	0.67286	0.132
transgenic ySAMdc/azygous control (red)	0.92149	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.13435	0.036

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.64696	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.87827	1
Manapal/WT (break)	0.66404	0.333
Manapal/WT (red)	0.74439	0.188