TnSeqCorr

• These are correlations of TnSeq responses across 82 experimental conditions.
• LFCs (log2-fold-changes) were computed for each gene in each condition relative to a relevant control condition (e.g. H37Rv grown on 7H9).
• The LFCs were normalized by dividing by the standard deviation for each condition. (so roughly, |LFC|>2 are the outliers, i.e. tails of the distribution)
• Note that essential genes often have LFCs around 0.
• Data for some genes is not available if they have less than 3 TA sites, or the dynamic range of LFCs is less than 2.0 across all conditions. (This is the case for many essential genes.)
• 'leverage' on each plot is a statistical score that indicates how much the regression is influenced by a few outlier points; the traditional threshold is indicated on the plots (3p/n, which is about 0.07 for this dataset), but in practice, cases with leverage > ~0.2 seem to be the least reliable (most misleading) correlation coefficients.

Top 10 genes with highest correlation to Rv3547/ddn:

update plot	correlation	link to info on gene
Rv1810/-	(cc=0.3693)	info on Rv1810/-
Rv1748/-	(cc=0.3647)	info on Rv1748/-
Rv2080/lppJ	(cc=0.3504)	info on Rv2080/lppJ
Rv1914c/-	(cc=0.3435)	info on Rv1914c/-
Rv3158/nuoN	(cc=0.337)	info on Rv3158/nuoN
Rv1472/echA12	(cc=0.3354)	info on Rv1472/echA12
Rv1951c/-	(cc=0.3263)	info on Rv1951c/-
Rv2456c/-	(cc=0.3259)	info on Rv2456c/-
Rv0755A/-	(cc=0.3256)	info on Rv0755A/-
Rv1885c/-	(cc=0.3226)	info on Rv1885c/-

Correlation of Rv3547/ddn with Rv1748/-

Normalized LFCs for Rv3547/ddn:
(description and provenance of datasets)

	Rv3547/ddn	Rv1748/-
Fe_supp_jason_reseq	-0.3	0.111
low_pH_jason_reseq	-0.744	-0.858
NO_jason_reseq	-0.129	0.184
B6_jason_reseq	1.055	-0.016
MHCII_jason_reseq	-0.104	0.442
Isoniazid02	-0.613	0.291
Rifampicin4	0.309	0.014
Ethambutol3	0.738	2.101
Meropenem3	-0.062	0.552
Vancomycin16	0.218	-0.085
Rv2680_day32	-0.01	-0.393
H37Rv_KO_MarP	0.591	0.947
hypoxia_3wks	0.0	0.279
hypoxia_6wks	-0.044	-0.37
glycerol	-0.459	0.652
cholesterol	-0.931	0.316
AJ	-0.113	0.592
Bibs02	-0.117	0.669
Bibs02c	0.106	-0.1
BL6	0.735	0.874
BL6a	0.6	0.633
BXD01	0.497	0.744
BXD010	-0.082	0.875
BXD011	0.065	0.557
BXD03	-0.1	0.565
BXD04	0.734	1.697
BXD05	-0.191	0.33
BXD06	0.08	0.573
BXD07	0.547	0.952
BXD08	0.249	1.296
BXD09	0.386	0.669
CAST	0.269	-0.12
CCcont	0.376	0.687
DS01	-0.236	0.371
DS02	-0.205	-0.134
DS04	0.063	0.703
DS0c	-0.456	0.581
GP01	-0.466	0.384
GP02	0.162	0.45
GP0c	0.173	0.467
NOD	-0.177	0.112
NZO	-0.826	0.066
PWK	-0.705	0.098
H37Rv_KO_CtpC	-0.179	0.331
H37Rv_KO_CtpD	-0.814	-0.505
H37Rv_KO_Rv1272	1.26	0.336
H37Rv_KO_SugABC	0.773	1.04
H37Rv_KO_MbtN	0.652	0.788
Trans05	0.638	1.171
macrophage_unactivated	0.619	0.71
IL1	-0.323	-0.231
Rapamycin	0.068	0.335
Tcell	0.766	0.068
GMCSF	-0.288	0.869
IFNab	-0.635	0.063
IFNg	-0.061	-0.257
IFNg_GMCSF1	-0.17	0.053
Rv1432_day32	-0.275	-0.379
Rv1565c_day32	0.324	0.851
secA2_input	0.64	0.197
delta_Rv3594	0.415	0.545
delta_Rv3717	-0.083	0.398
delta_Rv3811	-0.336	0.281
delta_Rv0954	0.376	0.488
PonA1	0.893	0.495
EccD1_KO	0.27	-0.059
EspI_KO	-0.573	0.051
PE35_KO	-0.038	-0.064
PPE68_KO	0.243	0.07
glycerol2	0.157	-0.671
lignocerate	0.432	-0.192
oleate	0.129	0.153
phosphatidylcholine	0.345	-0.062
acetate	-0.203	-0.953
glucAc	0.012	-0.916
Rv0950ko	0.133	1.073
Rv1096ko	0.35	0.015
Rv3684ko	-0.92	0.619
delta_otsA_trehalose	0.054	-0.348