Tomato Functional Genomics Database (TFGD)

Expression of 1-1-4.3.19.12

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.98047	0.788
27DAP/17DAP	0.81739	0.532
39DAP/27DAP	1.57011	0.098
41DAP/39DAP	0.90905	0.615
42DAP/41DAP	1.16181	0.916
43DAP/42DAP	1.16547	1
47DAP/43DAP	0.89709	0.645
52DAP/47DAP	0.86951	0.6
57DAP/52DAP	1.31192	0.972

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.05906	0.928
17DAP/reference	1.07631	0.957
27DAP/reference	0.96167	0.623
39DAP/reference	0.97846	0.72
41DAP/reference	0.90916	0.434
42DAP/reference	1.03947	0.812
43DAP/reference	1.07693	0.812
47DAP/reference	1.06115	0.391
52DAP/reference	1.11924	0.576
57DAP/reference	0.2914

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.03054	0.99
27DAP/17DAP	1.03217	0.98
39DAP/27DAP	0.83341	0.377
41DAP/39DAP	0.96835	0.973
42DAP/41DAP	1.04576	0.927
43DAP/42DAP	0.9914	0.96
47DAP/43DAP	0.99976	0.985
52DAP/47DAP	0.95803	0.824
57DAP/52DAP	0.71947	0.159
57DAP/7DAP	1.31022	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.96313	0.55
17DAP/reference	0.86784	0.049
27DAP/reference	0.92291	0.185
39DAP/reference	1.01935	1
41DAP/reference	1.11744	0.402
42DAP/reference	0.95592	0.371
43DAP/reference	0.97723	0.48
47DAP/reference	1.03918	1
52DAP/reference	1.01521	1
57DAP/reference	0.92589	0.183

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.91397	0.426
17DAP/reference	0.94976	0.487
27DAP/reference	1.12463	0.961
39DAP/reference	1.04919	1
41DAP/reference	1.14403	0.277
42DAP/reference	1.21764	0.254
43DAP/reference	1.02387	0.919
47DAP/reference	1.07391	0.675
52DAP/reference	1.03625	1
57DAP/reference	0.80684	0.01

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.04139	0.709
17DAP/reference	0.97895	0.658
27DAP/reference	0.97949	0.624
39DAP/reference	0.86561	0.054
41DAP/reference	0.97575	0.56
42DAP/reference	1.52169	0.382
43DAP/reference	1.02386	1
47DAP/reference	0.88029	0.24
52DAP/reference	0.85328	0.247
57DAP/reference	1.11058	0.694

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.01121	1
26DAP/20DAP	0.91548	1
34DAP/26DAP	1.00697	1
51DAP/34DAP	0.88313	0.563
52DAP/51DAP	1.18979	0.133
53DAP/52DAP	1.1103	0.97
55DAP/53DAP	1.14746	0.722
57DAP/55DAP	1.32137	0.393
62DAP/57DAP	1.05573	0.994
68DAP/62DAP	1.04381	0.834
68DAP/14DAP	0.91413

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	2.08067	0.014

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	1.55125	0.034
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	1.63592
Mature Eggplant/Ripe Tomato	1.30998	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.97907	0.961
1-1-2/M82	1.10782	1
12-2/M82	1.15856
12-4/M82	1.07097	1
1-3/M82	1.05003	1
2-1-1/M82	0.98632
2-1/M82	0.71132	0.322
2-6/M82	1.00542	1
3-2/M82	N/A	N/A
4-1-1/M82	0.99028	1
4-1/M82	1.24166
4-3-2/M82	0.96907	0.698
4-3/M82	1.08769
5-3/M82	0.96067	1
6-2/M82	0.94047
6-3/M82	1.0279	1
7-1/M82	N/A	N/A
7-2/M82	1.1113	0.385
9-3-2/M82	1.67325

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.00546	1
IL2-6/WTpooled	0.93882
IL7-5/WTpooled	1.04624	1
IL7-3/WTpooled	1.30431	0.362
IL12-4/WTpooled	1.10418	0.624
IL1-4/WTpooled	1.1424	0.426
WT/WTpooled	0.99496	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	1.02895	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.06317	0.914
DC3000/delta hrp 6h	N/A	N/A
DC3000/delta hrp 12h	0.91219	1
DC3000/delta hrp 24h	0.88935	0.085

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.88865	0.691
DC3000 delta B/DC3000 delta AB	1.01465	1

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

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

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

hybridization	ratio	FDR (corrected p value)
self-self	0.98684	1
Var 0h	0.9674	1
Var 12h I row2-row1	0.83811	0.353
Var 12h NI row2-row1	0.90876	0.713
Var 36h I row2-row1	1.11515	0.908
Var 36h NI row2-row1	0.93719	0.382
Var 60h I row2-row1	1.07383	0.562
Var 60h NI row2-row1	0.92888	0.756
Time course 0hI-0hNI	0.98658	0.962
Time course 12hI-12hNI	0.9643	0.698
Time course 36hI-36hNI	0.93801	0.274
Time course 60hI-60hNI	0.63376	0.009

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)	1.9241	0.921
transgenic ySAMdc/azygous control (breaker)	1.27433	1
transgenic ySAMdc/azygous control (red)	0.76068	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.10107	0.213

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	N/A	N/A
Manapal/WT (break)	N/A	N/A
Manapal/WT (red)	1.35992	0.222