Tomato Functional Genomics Database (TFGD)

Expression of 1-1-5.4.13.3

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.12932	0.801
27DAP/17DAP	1.02202	0.934
39DAP/27DAP	1.60788	0.374
41DAP/39DAP	1.12707	0.919
42DAP/41DAP	0.80554	1
43DAP/42DAP	0.82435	0.705
47DAP/43DAP	1.19316	0.715
52DAP/47DAP	0.68512	0.378
57DAP/52DAP	0.81935	0.622

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.96603	0.503
17DAP/reference	1.09456	0.161
27DAP/reference	1.06084	0.539
39DAP/reference	1.04803	0.393
41DAP/reference	1.01356	1
42DAP/reference	0.8877	0.01
43DAP/reference	0.9824	0.675
47DAP/reference	0.90165	0.05
52DAP/reference	0.83777	0.135
57DAP/reference	0.8088	0.036

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.8318	0.238
27DAP/17DAP	1.00135	0.969
39DAP/27DAP	1.02819	0.799
41DAP/39DAP	1.28963	0.849
42DAP/41DAP	1.03421	1
43DAP/42DAP	1.19579	0.042
47DAP/43DAP	1.08269	0.812
52DAP/47DAP	0.97088	0.898
57DAP/52DAP	0.84711	0.109
57DAP/7DAP	1.22781	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.89214	0.27
17DAP/reference	1.18208	0.035
27DAP/reference	1.04885	0.664
39DAP/reference	1.14643	0.086
41DAP/reference	0.98702	0.619
42DAP/reference	1.02299	0.686
43DAP/reference	1.08001	0.344
47DAP/reference	0.86738	0.168
52DAP/reference	1.15515	0.286
57DAP/reference	1.04428	0.851

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.91781	0.329
17DAP/reference	0.93005	0.26
27DAP/reference	0.98425	0.598
39DAP/reference	0.78826	0.028
41DAP/reference	0.854	0.056
42DAP/reference	0.99675	0.655
43DAP/reference	1.32021	0.17
47DAP/reference	1.11495	0.291
52DAP/reference	0.82484	0.047
57DAP/reference	0.9782	0.581

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.93309	0.391
17DAP/reference	1.04739	0.72
27DAP/reference	1.14164	0.12
39DAP/reference	1.10698	0.245
41DAP/reference	0.98801	0.754
42DAP/reference	0.91042	0.445
43DAP/reference	0.72906	0.071
47DAP/reference	0.92298	0.224
52DAP/reference	0.97431	0.69
57DAP/reference	0.74904	0.057

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.04566	1
26DAP/20DAP	0.86727	0.512
34DAP/26DAP	1.02665	1
51DAP/34DAP	0.97447	0.816
52DAP/51DAP	1.1105	0.295
53DAP/52DAP	1.0277	1
55DAP/53DAP	0.93994	0.577
57DAP/55DAP	1.10129	0.915
62DAP/57DAP	0.90011	0.871
68DAP/62DAP	1.18077	0.682
68DAP/14DAP	1.07874	0.936

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.30389	0.391

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	N/A	N/A
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	N/A	N/A
Mature Eggplant/Ripe Tomato	N/A	N/A

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.99427	1
1-1-2/M82	0.82734	0.804
12-2/M82	1.17037
12-4/M82	1.13909	0.694
1-3/M82	N/A	N/A
2-1-1/M82	1.41737
2-1/M82	N/A	N/A
2-6/M82	N/A	N/A
3-2/M82	N/A	N/A
4-1-1/M82	1.09835
4-1/M82	N/A	N/A
4-3-2/M82	N/A	N/A
4-3/M82	0.80817	1
5-3/M82	0.87103	0.395
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	0.88853	0.881
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	0.99398	1
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.97513	1
IL12-4/WTpooled	1.0419	1
IL1-4/WTpooled	0.77008
WT/WTpooled	0.94829	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	1.79974	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.0171	1
DC3000/delta hrp 6h	1.21765	0.631
DC3000/delta hrp 12h	0.97571	1
DC3000/delta hrp 24h	1.68645	0.027

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	2.18501
DC3000 delta B/DC3000 delta AB	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.18606	1
Exp 36h	0.88331	0.699
Exp 60h	1.0548	1

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

hybridization	ratio	FDR (corrected p value)
self-self	N/A	N/A
Var 0h	0.92323	1
Var 12h I row2-row1	1.17864	0.736
Var 12h NI row2-row1	2.00826
Var 36h I row2-row1	0.65736	0.805
Var 36h NI row2-row1	0.66517	0.225
Var 60h I row2-row1	0.54562
Var 60h NI row2-row1	0.83514	0.458
Time course 0hI-0hNI	1.03252	0.799
Time course 12hI-12hNI	1.58086	0.036
Time course 36hI-36hNI	2.71413	0.005
Time course 60hI-60hNI	3.86267	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)	1.49702	0.297
transgenic ySAMdc/azygous control (breaker)	3.08876	1
transgenic ySAMdc/azygous control (red)	1.85938	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.89544	0.058

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.90634	0.222

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	3.07616	0.083
Manapal/WT (break)	1.95832	0.14
Manapal/WT (red)	0.85566	0.424