Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.3.6.9

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.00275	0.788
27DAP/17DAP	0.61638	0.04
39DAP/27DAP	1.12331	0.75
41DAP/39DAP	0.95646	0.761
42DAP/41DAP	1.20619	0.903
43DAP/42DAP	1.04004	1
47DAP/43DAP	0.8384	0.48
52DAP/47DAP	0.95368	0.865
57DAP/52DAP	0.85753	0.86

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.84681	0.115
17DAP/reference	0.8847	0.091
27DAP/reference	1.02552	0.88
39DAP/reference	1.12606	0.256
41DAP/reference	0.89838	0.201
42DAP/reference	1.0787	0.166
43DAP/reference	1.20102	0.064
47DAP/reference	1.41354	0.001
52DAP/reference	1.46379	0.008
57DAP/reference	1.30118	0.008

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.05094	0.858
27DAP/17DAP	1.10317	0.831
39DAP/27DAP	0.99318	0.984
41DAP/39DAP	0.90386	0.68
42DAP/41DAP	0.99637	0.845
43DAP/42DAP	1.1554	0.192
47DAP/43DAP	0.90375	0.41
52DAP/47DAP	1.30333	0.444
57DAP/52DAP	0.89997	0.598
57DAP/7DAP	0.91916

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.01946	1
17DAP/reference	1.25465	0.399
27DAP/reference	1.37432	0.16
39DAP/reference	1.1354	0.601
41DAP/reference	1.21681	0.083
42DAP/reference	0.92138	0.086
43DAP/reference	1.00744	0.665
47DAP/reference	1.26814	0.142
52DAP/reference	1.11502	0.401
57DAP/reference	1.15264	0.183

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.81702	0.093
17DAP/reference	0.81995	0.08
27DAP/reference	1.07179	1
39DAP/reference	1.0238	1
41DAP/reference	0.97605	0.422
42DAP/reference	0.97542	0.433
43DAP/reference	1.00432	0.706
47DAP/reference	1.27378	0.124
52DAP/reference	0.97313	0.351
57DAP/reference	0.98337	0.649

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.20396	0.287
17DAP/reference	0.93675	0.519
27DAP/reference	1.2902	0.038
39DAP/reference	1.13116	0.163
41DAP/reference	1.25522	0.06
42DAP/reference	1.31094	0.074
43DAP/reference	1.07223	0.768
47DAP/reference	1.16095	0.12
52DAP/reference	1.49372	0.085
57DAP/reference	1.57412	0.032

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.83771	0.26
26DAP/20DAP	1.823	0.099
34DAP/26DAP	0.76192	0.44
51DAP/34DAP	1.37577	0.224
52DAP/51DAP	1.25828	0.15
53DAP/52DAP	0.93698	0.732
55DAP/53DAP	1.19778	0.964
57DAP/55DAP	0.95621	0.78
62DAP/57DAP	1.30642	0.767
68DAP/62DAP	1.22377	0.899
68DAP/14DAP	1.31814	0.328

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.31113	0.057

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.47948	0.088
Mature Green Tomato/Ripe Tomato	1.40189	0.03
Immature Eggplant/Mature Eggplant	1.2819	0.05
Ripe Pepper/Ripe Tomato	1.40583	1
Mature Eggplant/Ripe Tomato	1.29459	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.95895	0.934
1-1-2/M82	1.21514	1
12-2/M82	1.08433	1
12-4/M82	0.83256	1
1-3/M82	1.36291	0.248
2-1-1/M82	0.85244	1
2-1/M82	0.92492	1
2-6/M82	0.87289	1
3-2/M82	1.94788
4-1-1/M82	0.87596	1
4-1/M82	N/A	N/A
4-3-2/M82	1.03056	1
4-3/M82	1.18004	1
5-3/M82	1.0441	1
6-2/M82	1.44541
6-3/M82	1.08665	1
7-1/M82	1.4537	0.598
7-2/M82	0.90723
9-3-2/M82	1.00581	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.99875	1
IL2-6/WTpooled	1.07466	0.788
IL7-5/WTpooled	0.76205	1
IL7-3/WTpooled	0.86259	0.31
IL12-4/WTpooled	0.78518	0.52
IL1-4/WTpooled	1.05209	1
WT/WTpooled	0.83891	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	1.06218	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.00103	1
DC3000/delta hrp 6h	1.16201	1
DC3000/delta hrp 12h	1.14665	1
DC3000/delta hrp 24h	0.81148	0.062

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.92863	0.629
DC3000 delta B/DC3000 delta AB	0.78762	0.035

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.21692	0.228
Exp 36h	1.39824	0.349
Exp 60h	2.00904	0.283

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

hybridization	ratio	FDR (corrected p value)
self-self	1.01641	1
Var 0h	0.89166	1
Var 12h I row2-row1	0.80801	0.338
Var 12h NI row2-row1	0.97381	0.906
Var 36h I row2-row1	0.78589	0.805
Var 36h NI row2-row1	1.55945	1
Var 60h I row2-row1	0.91539	0.952
Var 60h NI row2-row1	1.16148	0.904
Time course 0hI-0hNI	0.92718	0.548
Time course 12hI-12hNI	1.10714	0.461
Time course 36hI-36hNI	0.91982	0.15
Time course 60hI-60hNI	0.34235	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)	1.01474	0.921
transgenic ySAMdc/azygous control (breaker)	1.1507	0.248
transgenic ySAMdc/azygous control (red)	0.85823	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.06383	0.372

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.85386	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.76682	0.172
Manapal/WT (break)	0.83266	1
Manapal/WT (red)	1.0632	0.413