Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.2.8.7

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.52915	0.133
27DAP/17DAP	1.12313	0.845
39DAP/27DAP	1.19993	0.583
41DAP/39DAP	0.78912	0.264
42DAP/41DAP	1.21851	0.681
43DAP/42DAP	1.15966	0.869
47DAP/43DAP	0.93667	0.768
52DAP/47DAP	0.88756	0.673
57DAP/52DAP	1.26414	0.948

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.81151	0.08
17DAP/reference	1.05877	0.27
27DAP/reference	1.39796	0.013
39DAP/reference	1.06096	0.393
41DAP/reference	1.11394	0.158
42DAP/reference	1.48818	0.001
43DAP/reference	1.43569	0.022
47DAP/reference	1.4604	0.002
52DAP/reference	1.30275	0.011
57DAP/reference	1.11945	0.02

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.22534	0.103
27DAP/17DAP	1.01809	0.957
39DAP/27DAP	0.97398	0.737
41DAP/39DAP	0.88912	0.42
42DAP/41DAP	1.03116	0.763
43DAP/42DAP	1.01501	0.554
47DAP/43DAP	1.02559	0.884
52DAP/47DAP	0.96648	0.902
57DAP/52DAP	0.96932	0.716
57DAP/7DAP	1.15316	0.365

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.03542	0.961
17DAP/reference	1.16574	0.023
27DAP/reference	1.2119	0.007
39DAP/reference	1.04781	0.511
41DAP/reference	1.05189
42DAP/reference	1.02342	0.534
43DAP/reference	1.11362	0.873
47DAP/reference	1.58084	0.254
52DAP/reference	2.08966
57DAP/reference	1.22467	0.094

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.67356	0.007
17DAP/reference	1.37376	0.07
27DAP/reference	1.572	0.021
39DAP/reference	1.48986	0.013
41DAP/reference	1.42947	0.07
42DAP/reference	1.49586	0.008
43DAP/reference	0.94911	0.494
47DAP/reference	1.25626	0.017
52DAP/reference	1.47619	0.006
57DAP/reference	1.03447	0.916

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.06283	0.366
17DAP/reference	1.11533	0.337
27DAP/reference	1.2448	0.028
39DAP/reference	1.30116	0.017
41DAP/reference	1.23951	0.038
42DAP/reference	1.45523	0.04
43DAP/reference	1.3839	0.068
47DAP/reference	1.17711	0.032
52DAP/reference	1.12566	0.301
57DAP/reference	1.89152	0.018

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.06705	0.966
26DAP/20DAP	1.23685	0.293
34DAP/26DAP	0.8592	0.153
51DAP/34DAP	0.78557	0.06
52DAP/51DAP	0.95624	1
53DAP/52DAP	N/A	N/A
55DAP/53DAP	0.89466	0.023
57DAP/55DAP	0.92092	0.691
62DAP/57DAP	1.01099	0.935
68DAP/62DAP	1.15504	0.523
68DAP/14DAP	1.17073	0.739

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	2.81176

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.98456	0.826
Mature Green Tomato/Ripe Tomato	0.86146	0.02
Immature Eggplant/Mature Eggplant	0.68403	0.096
Ripe Pepper/Ripe Tomato	0.24181	0.224
Mature Eggplant/Ripe Tomato	0.18531	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.97081	0.961
1-1-2/M82	0.93851	1
12-2/M82	0.96087	0.955
12-4/M82	0.99616	1
1-3/M82	0.9535	0.441
2-1-1/M82	0.84407	0.465
2-1/M82	0.94067	1
2-6/M82	0.91293	1
3-2/M82	1.01555	0.967
4-1-1/M82	0.91204	1
4-1/M82	1.10231	1
4-3-2/M82	0.97505	1
4-3/M82	0.89822	0.72
5-3/M82	0.96037	1
6-2/M82	1.021	1
6-3/M82	1.01973	1
7-1/M82	1.08617	0.992
7-2/M82	0.89112	0.796
9-3-2/M82	0.98884	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.17416
IL12-4/WTpooled	0.83247	0.581
IL1-4/WTpooled	1.38667	1
WT/WTpooled	1.08788	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	0.95946	0.75

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.12875	0.894
DC3000/delta hrp 6h	1.03418	1
DC3000/delta hrp 12h	0.98899	1
DC3000/delta hrp 24h	1.02565	0.797

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.07845	0.25
DC3000 delta B/DC3000 delta AB	1.08804	0.389

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.82254	1
Exp 36h	1.05284	1
Exp 60h	1.09556	1

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

hybridization	ratio	FDR (corrected p value)
self-self	0.97495	1
Var 0h	N/A	N/A
Var 12h I row2-row1	1.01437	0.692
Var 12h NI row2-row1	0.99827	1
Var 36h I row2-row1	1.08912	1
Var 36h NI row2-row1	1.28677	1
Var 60h I row2-row1	1.07967	1
Var 60h NI row2-row1	1.04636	1
Time course 0hI-0hNI	0.98174	0.94
Time course 12hI-12hNI	0.93845	0.169
Time course 36hI-36hNI	0.94714	0.206
Time course 60hI-60hNI	0.9702	0.646

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)	1.16953	0.654
transgenic ySAMdc/azygous control (breaker)	1.07983	1
transgenic ySAMdc/azygous control (red)	0.99718	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.06179	0.035

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.64118	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.17281	0.14
Manapal/WT (break)	1.02786	1
Manapal/WT (red)	1.0318	1