Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.2.13.13

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.09978	0.878
27DAP/17DAP	1.12919	0.927
39DAP/27DAP	0.78732	0.397
41DAP/39DAP	1.33242	0.426
42DAP/41DAP	1.06377	1
43DAP/42DAP	1.03252	0.948
47DAP/43DAP	0.99003	0.902
52DAP/47DAP	1.38188	0.466
57DAP/52DAP	1.00716	0.983

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.98243	0.578
17DAP/reference	1.0142	0.399
27DAP/reference	0.97811	0.497
39DAP/reference	1.05294	0.453
41DAP/reference	0.97316	0.434
42DAP/reference	0.93305	0.034
43DAP/reference	1.02568	0.758
47DAP/reference	0.95246	0.027
52DAP/reference	0.94144	0.21
57DAP/reference	0.96801	0.34

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.00056	1
27DAP/17DAP	0.99487	0.887
39DAP/27DAP	1.04728	0.643
41DAP/39DAP	1.0052	1
42DAP/41DAP	0.99653	0.907
43DAP/42DAP	0.9829	0.709
47DAP/43DAP	1.00643	0.951
52DAP/47DAP	1.00245	1
57DAP/52DAP	1.01171	0.971
57DAP/7DAP	1.05035	0.365

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.96276	0.27
17DAP/reference	0.9696	0.253
27DAP/reference	0.95324	0.125
39DAP/reference	0.98608	0.264
41DAP/reference	1.03028	0.812
42DAP/reference	0.88675
43DAP/reference	0.91054	0.025
47DAP/reference	0.87883	0.04
52DAP/reference	0.91226	0.232
57DAP/reference	1.00348	1

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.99468	0.907
17DAP/reference	1.03967	0.613
27DAP/reference	0.95274	0.317
39DAP/reference	0.90953	0.072
41DAP/reference	0.89697	0.183
42DAP/reference	1.03047	0.715
43DAP/reference	0.98182	0.592
47DAP/reference	1.01342	0.712
52DAP/reference	0.91619	0.023
57DAP/reference	0.98537	0.61

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.02639	0.691
17DAP/reference	0.92685	0.234
27DAP/reference	0.9631	0.092
39DAP/reference	0.94965	0.122
41DAP/reference	0.94647	0.167
42DAP/reference	0.89681	0.22
43DAP/reference	0.96195	0.319
47DAP/reference	0.98637	0.574
52DAP/reference	0.95736	0.529
57DAP/reference	0.92299	0.104

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.95054	0.841
26DAP/20DAP	0.90145	0.244
34DAP/26DAP	0.91411	0.404
51DAP/34DAP	0.97128	0.758
52DAP/51DAP	0.9862	1
53DAP/52DAP	0.9909	0.97
55DAP/53DAP	0.94783	0.376
57DAP/55DAP	0.99557	0.955
62DAP/57DAP	1.21802	0.393
68DAP/62DAP	0.91731	0.722
68DAP/14DAP	1.15441	0.521

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.97608	0.466

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.94409
Mature Green Tomato/Ripe Tomato	1.00362	1
Immature Eggplant/Mature Eggplant	1.95356	0.165
Ripe Pepper/Ripe Tomato	2.24472	0.258
Mature Eggplant/Ripe Tomato	1.09983	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.03155	1
1-1-2/M82	0.9445	1
12-2/M82	1.00623	1
12-4/M82	0.88741	1
1-3/M82	0.88837	0.441
2-1-1/M82	1.03334	1
2-1/M82	1.20066
2-6/M82	0.94741	1
3-2/M82	0.92995	1
4-1-1/M82	0.99733	1
4-1/M82	0.86871	1
4-3-2/M82	0.85186	0.698
4-3/M82	1.06403	1
5-3/M82	1.02538	1
6-2/M82	0.97414	1
6-3/M82	1.01175	1
7-1/M82	1.02792	1
7-2/M82	1.02168	1
9-3-2/M82	0.81346	0.355

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	0.9767	1
IL7-5/WTpooled	0.82873
IL7-3/WTpooled	0.85988	0.418
IL12-4/WTpooled	1.24159	0.673
IL1-4/WTpooled	1.13524	1
WT/WTpooled	0.99226	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	0.84852	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.03921	0.921
DC3000/delta hrp 6h	0.8762	0.95
DC3000/delta hrp 12h	0.99702	1
DC3000/delta hrp 24h	0.97671	0.875

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.19932	0.047
DC3000 delta B/DC3000 delta AB	1.20381	0.198

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.07994	0.227
Exp 36h	1.28215	0.693
Exp 60h	1.2825	0.399

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

hybridization	ratio	FDR (corrected p value)
self-self	0.94713	1
Var 0h	0.84045	0.332
Var 12h I row2-row1	1.17689	0.215
Var 12h NI row2-row1	1.02051	1
Var 36h I row2-row1	1.07539	1
Var 36h NI row2-row1	0.93305	0.61
Var 60h I row2-row1	1.06924	1
Var 60h NI row2-row1	0.90211	0.818
Time course 0hI-0hNI	1.09585	0.833
Time course 12hI-12hNI	1.0609	0.72
Time course 36hI-36hNI	1.05022	0.453
Time course 60hI-60hNI	1.48857	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)	0.99799	1
transgenic ySAMdc/azygous control (breaker)	1.12414	1
transgenic ySAMdc/azygous control (red)	1.12176	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.98053	0.149

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.13754	0.277

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.89102	1
Manapal/WT (break)	0.99126	1
Manapal/WT (red)	1.12513	1