Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.4.10.11

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.65552	0.057
27DAP/17DAP	1.391	0.646
39DAP/27DAP	0.9204	0.529
41DAP/39DAP	1.06174	0.949
42DAP/41DAP	0.94161	1
43DAP/42DAP	1.06961	0.945
47DAP/43DAP	1.16488	0.926
52DAP/47DAP	1.00132	0.92
57DAP/52DAP	0.83667	0.764

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.20298	0.024
17DAP/reference	0.1303	0.006
27DAP/reference	0.1716	0.009
39DAP/reference	0.26243	0.01
41DAP/reference	0.18576	0.008
42DAP/reference	0.29946	0.001
43DAP/reference	0.26459	0.013
47DAP/reference	0.2182	0.001
52DAP/reference	0.24272	0.014
57DAP/reference	0.32202	0.009

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.86248	0.402
27DAP/17DAP	1.11545	1
39DAP/27DAP	0.96754	0.812
41DAP/39DAP	0.90071	0.696
42DAP/41DAP	1.25926	0.622
43DAP/42DAP	1.18881	0.627
47DAP/43DAP	1.31658	0.664
52DAP/47DAP	1.11192	0.696
57DAP/52DAP	1.08804	0.783
57DAP/7DAP	1.34584	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.74216	0.224
17DAP/reference	1.07671	0.525
27DAP/reference	1.13908	0.107
39DAP/reference	1.33703	0.021
41DAP/reference	1.97281	0.097
42DAP/reference	1.55665	0.013
43DAP/reference	1.56777	0.105
47DAP/reference	0.66283	0.168
52DAP/reference	1.27471	0.491
57DAP/reference	0.71826	0.027

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.46614	0.022
17DAP/reference	0.24232	0.003
27DAP/reference	0.34142	0.007
39DAP/reference	0.37606	0.03
41DAP/reference	0.44153	0.007
42DAP/reference	0.33091	0.011
43DAP/reference	0.28501	0.002
47DAP/reference	0.32961	0.008
52DAP/reference	0.31487	0.007
57DAP/reference	0.31013	0.005

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.79536	0.214
17DAP/reference	0.54227	0.139
27DAP/reference	0.8136	0.174
39DAP/reference	0.814	0.222
41DAP/reference	0.8079	0.237
42DAP/reference	0.78345	0.172
43DAP/reference	0.70285	0.158
47DAP/reference	0.15569	0.004
52DAP/reference	0.90116	0.334
57DAP/reference	0.44258	0.023

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.95522	1
26DAP/20DAP	0.93821	1
34DAP/26DAP	N/A	N/A
51DAP/34DAP	1.61272	0.946
52DAP/51DAP	1.55397	0.126
53DAP/52DAP	1.22553	0.806
55DAP/53DAP	1.18719	0.434
57DAP/55DAP	1.19768	0.745
62DAP/57DAP	1.16494	0.622
68DAP/62DAP	0.98708	0.863
68DAP/14DAP	0.86667	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.42479	0.229

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	1.25803	0.591
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	0.66379
2-1-1/M82	N/A	N/A
2-1/M82	N/A	N/A
2-6/M82	0.95406
3-2/M82	N/A	N/A
4-1-1/M82	0.90087
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	0.95605	0.23
6-2/M82	N/A	N/A
6-3/M82	0.6767	1
7-1/M82	N/A	N/A
7-2/M82	0.44631
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.09701	0.277
IL2-6/WTpooled	1.1985	0.531
IL7-5/WTpooled	1.08048	0.792
IL7-3/WTpooled	1.03022	1
IL12-4/WTpooled	0.96523	1
IL1-4/WTpooled	1.12071	1
WT/WTpooled	0.93962	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	0.91887	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.96586	1
DC3000/delta hrp 6h	1.26566	0.978
DC3000/delta hrp 12h	0.36853	1
DC3000/delta hrp 24h	4.90795	0.028

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.53588	0.06
DC3000 delta B/DC3000 delta AB	1.37534	0.166

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	N/A	N/A
Exp 36h	0.5077	0.623
Exp 60h	0.31824	0.249

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

hybridization	ratio	FDR (corrected p value)
self-self	1.07347
Var 0h	1.13579	0.374
Var 12h I row2-row1	1.20899	0.58
Var 12h NI row2-row1	0.90465	0.713
Var 36h I row2-row1	0.85361	0.575
Var 36h NI row2-row1	1.11134	1
Var 60h I row2-row1	1.00867	1
Var 60h NI row2-row1	0.74865	0.904
Time course 0hI-0hNI	0.88763	0.384
Time course 12hI-12hNI	1.01344	1
Time course 36hI-36hNI	0.95475	0.433
Time course 60hI-60hNI	0.51027	0.006

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)	0.97753	0.722
transgenic ySAMdc/azygous control (breaker)	3.50796	0.248
transgenic ySAMdc/azygous control (red)	1.09884	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.94785	0.101

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.99512	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.38334	0.14
Manapal/WT (break)	N/A	N/A
Manapal/WT (red)	N/A	N/A