Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.1.2.19

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.96624	0.713
27DAP/17DAP	0.87228	0.69
39DAP/27DAP	1.44861	0.579
41DAP/39DAP	0.9543	0.807
42DAP/41DAP	1.00953	1
43DAP/42DAP	0.96106	0.888
47DAP/43DAP	1.21701	0.576
52DAP/47DAP	1.3041	0.773
57DAP/52DAP	1.42442	0.894

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.16993	0.707
17DAP/reference	1.22102	0.048
27DAP/reference	1.03441	0.863
39DAP/reference	0.96616	0.6
41DAP/reference	1.25069	0.158
42DAP/reference	1.46101	0.004
43DAP/reference	1.27739	0.617
47DAP/reference	1.43233	0.002
52DAP/reference	1.34743	0.008
57DAP/reference	1.19483	0.088

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.19773	0.061
27DAP/17DAP	0.93349	0.724
39DAP/27DAP	0.88249	0.211
41DAP/39DAP	0.96427	0.923
42DAP/41DAP	1.17974	0.622
43DAP/42DAP	0.81582	0.143
47DAP/43DAP	0.87925	0.305
52DAP/47DAP	1.67035	0.142
57DAP/52DAP	2.11981	0.109
57DAP/7DAP	1.33504	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.86078	0.146
17DAP/reference	1.1268	0.297
27DAP/reference	0.96862	0.375
39DAP/reference	1.08028	0.601
41DAP/reference	1.20698	0.35
42DAP/reference	1.15619	0.686
43DAP/reference	1.17692	0.256
47DAP/reference	1.1844	0.219
52DAP/reference	0.95533	0.435
57DAP/reference	0.9784	0.477

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.38267	0.17
17DAP/reference	1.8111	0.009
27DAP/reference	1.39854	0.062
39DAP/reference	1.12106	0.686
41DAP/reference	1.5417	0.006
42DAP/reference	1.2509	0.036
43DAP/reference	1.27008	0.093
47DAP/reference	1.08736	0.513
52DAP/reference	1.09182	0.747
57DAP/reference	1.32744	0.2

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.22416	0.153
17DAP/reference	1.07129	0.887
27DAP/reference	0.97502	0.566
39DAP/reference	1.0836	0.912
41DAP/reference	1.01775	1
42DAP/reference	1.17728	0.307
43DAP/reference	1.46585	0.121
47DAP/reference	1.06496	1
52DAP/reference	1.05072	0.928
57DAP/reference	1.07995	0.758

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.07499	0.817
26DAP/20DAP	1.40328	1
34DAP/26DAP	3.28796	0.819
51DAP/34DAP	1.70904	0.829
52DAP/51DAP	4.98869	0.034
53DAP/52DAP	0.70607	0.055
55DAP/53DAP	1.6343	0.027
57DAP/55DAP	0.59938	0.066
62DAP/57DAP	0.29045
68DAP/62DAP	0.46835
68DAP/14DAP	1.8317	0.346

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.2175	0.02

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.14011
Mature Green Tomato/Ripe Tomato	0.68304	0.055
Immature Eggplant/Mature Eggplant	0.63763	0.063
Ripe Pepper/Ripe Tomato	N/A	N/A
Mature Eggplant/Ripe Tomato	0.82063	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	3.56633	0.409
1-1-2/M82	1.18386	1
12-2/M82	1.27143	1
12-4/M82	0.67516	1
1-3/M82	1.12158	1
2-1-1/M82	1.56432	1
2-1/M82	0.49094	0.322
2-6/M82	2.34808	0.385
3-2/M82	0.18728
4-1-1/M82	2.2367	1
4-1/M82	0.35131
4-3-2/M82	N/A	N/A
4-3/M82	1.7229	1
5-3/M82	0.63676	0.49
6-2/M82	1.02489	1
6-3/M82	0.5685	0.916
7-1/M82	0.62442	0.509
7-2/M82	1.97824	0.318
9-3-2/M82	0.74997

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.02899	1
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	1.16543	0.792
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	N/A	N/A
IL1-4/WTpooled	1.39037
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	0.94982	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.00164	1
DC3000/delta hrp 6h	1.1892	1
DC3000/delta hrp 12h	1.54838	1
DC3000/delta hrp 24h	0.66454	0.036

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.22318	0.076
DC3000 delta B/DC3000 delta AB	1.32242	0.177

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.79415	1
Exp 36h	0.96284	0.879
Exp 60h	1.23625	0.563

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

hybridization	ratio	FDR (corrected p value)
self-self	1.00727	1
Var 0h	0.91818	1
Var 12h I row2-row1	0.77927	0.565
Var 12h NI row2-row1	0.88277	0.82
Var 36h I row2-row1	1.08413	1
Var 36h NI row2-row1	1.53014	0.276
Var 60h I row2-row1	1.08901	1
Var 60h NI row2-row1	0.94906	1
Time course 0hI-0hNI	0.89406	0.376
Time course 12hI-12hNI	1.00895	1
Time course 36hI-36hNI	0.95452	0.433
Time course 60hI-60hNI	0.87329	0.047

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)	1.14	0.384
transgenic ySAMdc/azygous control (breaker)	1.32754	0.248
transgenic ySAMdc/azygous control (red)	1.15962	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.9755	0.631

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.98716	0.789

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.20907	0.307
Manapal/WT (break)	1.12725	1
Manapal/WT (red)	1.31663	1