Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.1.19.17

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.94253	0.551
27DAP/17DAP	0.90916	0.784
39DAP/27DAP	0.9327	0.564
41DAP/39DAP	1.17531	0.708
42DAP/41DAP	1.06801	0.945
43DAP/42DAP	1.0681	1
47DAP/43DAP	1.04601	0.776
52DAP/47DAP	1.02884	0.976
57DAP/52DAP	1.02243	0.98

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.95665	0.412
17DAP/reference	0.92976	0.298
27DAP/reference	0.93771	0.119
39DAP/reference	1.01218	0.747
41DAP/reference	1.06756	0.024
42DAP/reference	1.03127	0.544
43DAP/reference	0.96104	0.247
47DAP/reference	1.03083	0.627
52DAP/reference	0.96897	0.416
57DAP/reference	0.87644	0.017

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.98291	0.732
27DAP/17DAP	1.01953	0.968
39DAP/27DAP	1.04066	0.615
41DAP/39DAP	0.96855	0.959
42DAP/41DAP	1.02882	0.886
43DAP/42DAP	1.08328	0.273
47DAP/43DAP	0.97156	0.764
52DAP/47DAP	1.00017	0.975
57DAP/52DAP	0.9636	0.657
57DAP/7DAP	1.02892	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.92158	0.071
17DAP/reference	0.98612	0.338
27DAP/reference	0.9798	0.348
39DAP/reference	0.9982	0.745
41DAP/reference	0.91426	0.194
42DAP/reference	0.8484	0.01
43DAP/reference	0.96856	0.403
47DAP/reference	0.86129	0.168
52DAP/reference	0.98252	0.621
57DAP/reference	0.97701	0.477

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.01486	0.885
17DAP/reference	0.9319	0.164
27DAP/reference	0.89719	0.167
39DAP/reference	0.95673	0.208
41DAP/reference	0.90487	0.11
42DAP/reference	0.86842	0.035
43DAP/reference	1.02638	0.827
47DAP/reference	0.88593	0.094
52DAP/reference	0.97525	0.407
57DAP/reference	1.02032	0.807

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.97576	0.391
17DAP/reference	0.9408	0.328
27DAP/reference	1.00671	0.934
39DAP/reference	0.95983	0.05
41DAP/reference	0.99644	0.826
42DAP/reference	0.92167	0.172
43DAP/reference	0.94882	0.305
47DAP/reference	0.88623	0.066
52DAP/reference	0.9245	0.405
57DAP/reference	0.67225	0.016

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.99914	1
26DAP/20DAP	0.93595	1
34DAP/26DAP	1.00532	1
51DAP/34DAP	1.04089	0.73
52DAP/51DAP	1.00199	1
53DAP/52DAP	0.99488	0.983
55DAP/53DAP	1.17617	0.429
57DAP/55DAP	0.94493	0.698
62DAP/57DAP	1.11599	0.569
68DAP/62DAP	0.9299	0.543
68DAP/14DAP	1.0912	0.521

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.90398	0.211

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.37715	0.863
Mature Green Tomato/Ripe Tomato	0.91957	0.487
Immature Eggplant/Mature Eggplant	1.80343	0.05
Ripe Pepper/Ripe Tomato	1.93937	1
Mature Eggplant/Ripe Tomato	2.91694	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.9176	0.944
1-1-2/M82	0.89766	0.958
12-2/M82	1.03615	1
12-4/M82	0.95994	1
1-3/M82	0.91065	0.441
2-1-1/M82	1.13798	1
2-1/M82	N/A	N/A
2-6/M82	1.08455	0.695
3-2/M82	0.95732
4-1-1/M82	1.08292	1
4-1/M82	0.84478	1
4-3-2/M82	0.94244	1
4-3/M82	0.70129	0.509
5-3/M82	0.93655	1
6-2/M82	0.98017	1
6-3/M82	1.05924	1
7-1/M82	N/A	N/A
7-2/M82	0.97278	1
9-3-2/M82	0.75296

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.87638	0.243
IL2-6/WTpooled	1.02589	1
IL7-5/WTpooled	1.1919	0.792
IL7-3/WTpooled	0.91323	1
IL12-4/WTpooled	1.23024	0.595
IL1-4/WTpooled	0.92228	0.457
WT/WTpooled	0.94692	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	0.91057	0.75

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.93901	1
DC3000/delta hrp 6h	0.92881	0.95
DC3000/delta hrp 12h	0.98886	1
DC3000/delta hrp 24h	0.9569	0.662

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.07842	0.441
DC3000 delta B/DC3000 delta AB	1.07458	0.449

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.98869	1
Exp 36h	1.30097	1
Exp 60h	1.16606	1

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

hybridization	ratio	FDR (corrected p value)
self-self	0.88441	1
Var 0h	0.72357	0.933
Var 12h I row2-row1	1.0553	0.379
Var 12h NI row2-row1	0.97271	0.906
Var 36h I row2-row1	0.89098	0.805
Var 36h NI row2-row1	0.77903	1
Var 60h I row2-row1	1.36396	0.562
Var 60h NI row2-row1	1.07943	0.904
Time course 0hI-0hNI	1.0438	0.799
Time course 12hI-12hNI	1.00657	0.888
Time course 36hI-36hNI	0.92284	0.142
Time course 60hI-60hNI	0.98623	1

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)	1.01637	0.612
transgenic ySAMdc/azygous control (breaker)	0.81702	0.251
transgenic ySAMdc/azygous control (red)	1.14056	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.99444	0.737

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.8893	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.37702	0.105
Manapal/WT (break)	0.84351	0.333
Manapal/WT (red)	0.69065	0.181