Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.4.2.6

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.40321	0.014
27DAP/17DAP	0.46298	0.04
39DAP/27DAP	1.37366	1
41DAP/39DAP	0.67588	0.095
42DAP/41DAP	0.8176	0.774
43DAP/42DAP	1.41997	0.26
47DAP/43DAP	0.93018	0.701
52DAP/47DAP	0.86069	0.673
57DAP/52DAP	1.60941	0.946

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.99252	0.727
17DAP/reference	0.84359	0.014
27DAP/reference	0.99037	0.725
39DAP/reference	0.7537	0.038
41DAP/reference	0.61998	0.008
42DAP/reference	0.83251	0.019
43DAP/reference	0.84061	0.049
47DAP/reference	0.9795	0.418
52DAP/reference	1.14454	0.286
57DAP/reference	1.6114	0.012

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.73538	0.348
27DAP/17DAP	0.92582	0.919
39DAP/27DAP	N/A	N/A
41DAP/39DAP	0.74638	0.861
42DAP/41DAP	2.20123	0.694
43DAP/42DAP	1.164	0.788
47DAP/43DAP	1.51907	0.618
52DAP/47DAP	1.0619	0.947
57DAP/52DAP	1.14428
57DAP/7DAP	1.11712

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	2.3888	0.024
17DAP/reference	1.5125	0.896
27DAP/reference	1.19914	0.026
39DAP/reference	1.06551	0.538
41DAP/reference	0.95652	0.247
42DAP/reference	1.16618	0.405
43DAP/reference	1.0512	0.923
47DAP/reference	0.96823	0.671
52DAP/reference	0.80521	0.012
57DAP/reference	0.91799	0.101

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.18343	0.642
17DAP/reference	0.88931	0.195
27DAP/reference	0.96708	0.501
39DAP/reference	0.81715	0.074
41DAP/reference	0.95672	0.315
42DAP/reference	0.89135	0.121
43DAP/reference	0.55281	0.003
47DAP/reference	0.8112	0.021
52DAP/reference	0.75619	0.005
57DAP/reference	0.52227	0.003

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	2.91137	0.02
17DAP/reference	1.59784	0.398
27DAP/reference	2.0699	0.016
39DAP/reference	1.1493	0.285
41DAP/reference	1.04188	0.714
42DAP/reference	0.89492	0.361
43DAP/reference	0.94782	0.449
47DAP/reference	0.912	0.296
52DAP/reference	0.63553	0.047
57DAP/reference	1.7064	0.008

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.13466	0.966
26DAP/20DAP	N/A	N/A
34DAP/26DAP	1.27046	1
51DAP/34DAP	0.9956	0.927
52DAP/51DAP	0.97115
53DAP/52DAP	1.40064
55DAP/53DAP	1.15167	0.645
57DAP/55DAP	0.6103	0.03
62DAP/57DAP	1.48423	0.021
68DAP/62DAP	2.98282	0.032
68DAP/14DAP	1.13677	0.826

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

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

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	4.75475	0.058
Mature Green Tomato/Ripe Tomato	6.71819	0.015
Immature Eggplant/Mature Eggplant	0.24503	0.062
Ripe Pepper/Ripe Tomato	11.8611	0.258
Mature Eggplant/Ripe Tomato	62.7093	0.268

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.21109	0.877
1-1-2/M82	1.0997	1
12-2/M82	1.36314	1
12-4/M82	0.87304	0.358
1-3/M82	1.03516
2-1-1/M82	N/A	N/A
2-1/M82	0.94918
2-6/M82	N/A	N/A
3-2/M82	0.85039	1
4-1-1/M82	N/A	N/A
4-1/M82	N/A	N/A
4-3-2/M82	N/A	N/A
4-3/M82	1.82447	0.268
5-3/M82	0.87106	1
6-2/M82	1.2412
6-3/M82	0.69988
7-1/M82	0.77336	0.452
7-2/M82	1.14746	1
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.37637	0.321
IL2-6/WTpooled	1.52713	0.456
IL7-5/WTpooled	0.83588	1
IL7-3/WTpooled	0.5042	0.298
IL12-4/WTpooled	0.87659	1
IL1-4/WTpooled	0.80862	0.415
WT/WTpooled	1.0336	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	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.00734	1
DC3000/delta hrp 6h	0.91761	0.95
DC3000/delta hrp 12h	1.09493	1
DC3000/delta hrp 24h	0.57485	0.059

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	N/A	N/A
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	0.92052	1
Exp 36h	0.67015	0.397
Exp 60h	0.58687	0.251

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	N/A	N/A
Var 12h I row2-row1	N/A	N/A
Var 12h NI row2-row1	N/A	N/A
Var 36h I row2-row1	N/A	N/A
Var 36h NI row2-row1	N/A	N/A
Var 60h I row2-row1	N/A	N/A
Var 60h NI row2-row1	N/A	N/A
Time course 0hI-0hNI	N/A	N/A
Time course 12hI-12hNI	N/A	N/A
Time course 36hI-36hNI	N/A	N/A
Time course 60hI-60hNI	N/A	N/A

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)	0.715	0.3
transgenic ySAMdc/azygous control (breaker)	1.96378	0.248
transgenic ySAMdc/azygous control (red)	1.12645	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.76119	0.087

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	3.88176	0.233

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.44658	0.105
Manapal/WT (break)	1.94773	0.381
Manapal/WT (red)	1.02442	1