Tomato Functional Genomics Database (TFGD)

Expression of 1-1-4.1.7.11

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.97482	0.64
27DAP/17DAP	1.5514	0.735
39DAP/27DAP	1.22608	0.8
41DAP/39DAP	0.67799	0.193
42DAP/41DAP	0.90646	1
43DAP/42DAP	1.11717	1
47DAP/43DAP	1.20356	0.856
52DAP/47DAP	1.0549	0.8
57DAP/52DAP	0.98879	0.982

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.23394	0.611
17DAP/reference	0.95067	0.567
27DAP/reference	0.97773	0.683
39DAP/reference	0.94316	0.513
41DAP/reference	0.89465	0.065
42DAP/reference	1.08386	0.523
43DAP/reference	1.05691	0.617
47DAP/reference	1.09369	0.365
52DAP/reference	1.27162	0.079
57DAP/reference	1.11852	0.405

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.95739	0.663
27DAP/17DAP	1.0125	0.969
39DAP/27DAP	1.14917	0.499
41DAP/39DAP	1.12738	0.849
42DAP/41DAP	1.02077	0.893
43DAP/42DAP	1.3518	0.351
47DAP/43DAP	1.0206	0.844
52DAP/47DAP	1.00898	1
57DAP/52DAP	0.99778	0.905
57DAP/7DAP	1.26252	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.16029	0.472
17DAP/reference	1.17144
27DAP/reference	N/A	N/A
39DAP/reference	N/A	N/A
41DAP/reference	1.09757
42DAP/reference	3.27191
43DAP/reference	1.25524	0.105
47DAP/reference	1.16185	0.149
52DAP/reference	0.99829
57DAP/reference	1.97499	0.004

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.01689	1
17DAP/reference	0.80271	0.047
27DAP/reference	1.05801	0.81
39DAP/reference	1.14363	0.099
41DAP/reference	0.97546	0.531
42DAP/reference	1.03988	1
43DAP/reference	0.89733	0.128
47DAP/reference	0.94993	0.4
52DAP/reference	1.36498	0.029
57DAP/reference	0.96384	0.338

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.99068	0.75
17DAP/reference	1.19911
27DAP/reference	1.56198	0.059
39DAP/reference	0.94355
41DAP/reference	1.24708	0.239
42DAP/reference	1.38531	0.013
43DAP/reference	1.50066	0.029
47DAP/reference	1.02957	0.754
52DAP/reference	N/A	N/A
57DAP/reference	1.3216	0.268

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.93236	1
26DAP/20DAP	0.34747	0.512
34DAP/26DAP	3.98954	1
51DAP/34DAP	2.01166	0.759
52DAP/51DAP	5.26578	0.033
53DAP/52DAP	0.85095	0.342
55DAP/53DAP	1.25335	0.046
57DAP/55DAP	0.64498	0.181
62DAP/57DAP	2.03718
68DAP/62DAP	N/A	N/A
68DAP/14DAP	1.18044	0.295

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.78622	0.129

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.71346	0.058
Mature Green Tomato/Ripe Tomato	N/A	N/A
Immature Eggplant/Mature Eggplant	0.40536	0.062
Ripe Pepper/Ripe Tomato	6.32601
Mature Eggplant/Ripe Tomato	N/A	N/A

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.98577	0.961
1-1-2/M82	N/A	N/A
12-2/M82	N/A	N/A
12-4/M82	N/A	N/A
1-3/M82	0.54888
2-1-1/M82	N/A	N/A
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	N/A	N/A
4-1/M82	N/A	N/A
4-3-2/M82	N/A	N/A
4-3/M82	N/A	N/A
5-3/M82	0.94683	1
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	N/A	N/A
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	1.44758	0.659
IL7-5/WTpooled	1.64329	0.75
IL7-3/WTpooled	1.05725	1
IL12-4/WTpooled	0.96163	1
IL1-4/WTpooled	1.10065	1
WT/WTpooled	1.00048	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	1.35529	0.309

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.95824	1
DC3000/delta hrp 6h	1.05575	1
DC3000/delta hrp 12h	0.96782	1
DC3000/delta hrp 24h	0.54763	0.034

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.14057	0.073
DC3000 delta B/DC3000 delta AB	1.01711	1

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.06865	1
Exp 36h	0.643	0.449
Exp 60h	0.58284	0.278

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

hybridization	ratio	FDR (corrected p value)
self-self	1.04264	1
Var 0h	0.9207	1
Var 12h I row2-row1	0.98356	0.948
Var 12h NI row2-row1	1.21228	0.649
Var 36h I row2-row1	1.21075	0.742
Var 36h NI row2-row1	1.05439	1
Var 60h I row2-row1	0.69051	0.292
Var 60h NI row2-row1	0.86734	0.932
Time course 0hI-0hNI	0.81982	0.219
Time course 12hI-12hNI	1.09564	1
Time course 36hI-36hNI	1.38562	0.975
Time course 60hI-60hNI	2.16722	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)	0.73623	0.289
transgenic ySAMdc/azygous control (breaker)	0.89099	0.173
transgenic ySAMdc/azygous control (red)	1.52458	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.06961	0.261

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.49303	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.30054	0.14
Manapal/WT (break)	1.90962	0.14
Manapal/WT (red)	1.02463	1