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 Rv2456c/-

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

	Rv3547/ddn	Rv2456c/-
Fe_supp_jason_reseq	-0.3	-0.379
low_pH_jason_reseq	-0.744	-1.086
NO_jason_reseq	-0.129	0.0
B6_jason_reseq	1.055	0.476
MHCII_jason_reseq	-0.104	-0.595
Isoniazid02	-0.613	0.215
Rifampicin4	0.309	0.143
Ethambutol3	0.738	0.591
Meropenem3	-0.062	-0.126
Vancomycin16	0.218	0.048
Rv2680_day32	-0.01	0.302
H37Rv_KO_MarP	0.591	0.071
hypoxia_3wks	0.0	-0.423
hypoxia_6wks	-0.044	0.355
glycerol	-0.459	-0.648
cholesterol	-0.931	0.259
AJ	-0.113	-0.224
Bibs02	-0.117	-0.301
Bibs02c	0.106	-0.076
BL6	0.735	0.922
BL6a	0.6	0.716
BXD01	0.497	0.662
BXD010	-0.082	0.612
BXD011	0.065	1.502
BXD03	-0.1	0.774
BXD04	0.734	1.111
BXD05	-0.191	0.484
BXD06	0.08	0.863
BXD07	0.547	0.971
BXD08	0.249	0.717
BXD09	0.386	0.702
CAST	0.269	0.929
CCcont	0.376	0.332
DS01	-0.236	-0.399
DS02	-0.205	0.0
DS04	0.063	-0.128
DS0c	-0.456	0.061
GP01	-0.466	0.393
GP02	0.162	0.291
GP0c	0.173	0.461
NOD	-0.177	0.428
NZO	-0.826	0.321
PWK	-0.705	0.186
H37Rv_KO_CtpC	-0.179	0.495
H37Rv_KO_CtpD	-0.814	-0.268
H37Rv_KO_Rv1272	1.26	0.562
H37Rv_KO_SugABC	0.773	-0.214
H37Rv_KO_MbtN	0.652	0.886
Trans05	0.638	1.071
macrophage_unactivated	0.619	-0.167
IL1	-0.323	0.077
Rapamycin	0.068	-0.009
Tcell	0.766	0.502
GMCSF	-0.288	0.185
IFNab	-0.635	-0.212
IFNg	-0.061	0.195
IFNg_GMCSF1	-0.17	0.031
Rv1432_day32	-0.275	0.149
Rv1565c_day32	0.324	-0.442
secA2_input	0.64	-0.092
delta_Rv3594	0.415	0.138
delta_Rv3717	-0.083	0.457
delta_Rv3811	-0.336	-0.303
delta_Rv0954	0.376	-0.521
PonA1	0.893	-0.433
EccD1_KO	0.27	0.556
EspI_KO	-0.573	0.114
PE35_KO	-0.038	-0.12
PPE68_KO	0.243	-0.266
glycerol2	0.157	0.338
lignocerate	0.432	0.813
oleate	0.129	0.386
phosphatidylcholine	0.345	0.829
acetate	-0.203	0.068
glucAc	0.012	0.289
Rv0950ko	0.133	0.416
Rv1096ko	0.35	0.329
Rv3684ko	-0.92	0.37
delta_otsA_trehalose	0.054	-1.403