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 Rv1885c/-

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

	Rv3547/ddn	Rv1885c/-
Fe_supp_jason_reseq	-0.3	-0.204
low_pH_jason_reseq	-0.744	-0.37
NO_jason_reseq	-0.129	-0.221
B6_jason_reseq	1.055	-0.127
MHCII_jason_reseq	-0.104	0.283
Isoniazid02	-0.613	-0.115
Rifampicin4	0.309	-0.574
Ethambutol3	0.738	0.129
Meropenem3	-0.062	0.028
Vancomycin16	0.218	-0.732
Rv2680_day32	-0.01	-0.112
H37Rv_KO_MarP	0.591	0.109
hypoxia_3wks	0.0	0.08
hypoxia_6wks	-0.044	-0.263
glycerol	-0.459	-0.252
cholesterol	-0.931	-0.495
AJ	-0.113	0.148
Bibs02	-0.117	-0.044
Bibs02c	0.106	-0.341
BL6	0.735	0.592
BL6a	0.6	-0.125
BXD01	0.497	-0.012
BXD010	-0.082	-0.281
BXD011	0.065	0.275
BXD03	-0.1	0.223
BXD04	0.734	0.864
BXD05	-0.191	0.115
BXD06	0.08	0.0
BXD07	0.547	0.346
BXD08	0.249	0.079
BXD09	0.386	0.09
CAST	0.269	0.01
CCcont	0.376	0.3
DS01	-0.236	-0.546
DS02	-0.205	-0.503
DS04	0.063	-0.994
DS0c	-0.456	-0.104
GP01	-0.466	-0.087
GP02	0.162	0.512
GP0c	0.173	0.172
NOD	-0.177	0.308
NZO	-0.826	0.24
PWK	-0.705	0.054
H37Rv_KO_CtpC	-0.179	0.418
H37Rv_KO_CtpD	-0.814	0.298
H37Rv_KO_Rv1272	1.26	0.94
H37Rv_KO_SugABC	0.773	0.908
H37Rv_KO_MbtN	0.652	0.927
Trans05	0.638	1.173
macrophage_unactivated	0.619	-0.019
IL1	-0.323	-0.839
Rapamycin	0.068	-0.298
Tcell	0.766	-0.098
GMCSF	-0.288	0.121
IFNab	-0.635	0.157
IFNg	-0.061	-0.08
IFNg_GMCSF1	-0.17	0.317
Rv1432_day32	-0.275	0.297
Rv1565c_day32	0.324	-0.608
secA2_input	0.64	-0.282
delta_Rv3594	0.415	0.219
delta_Rv3717	-0.083	-0.128
delta_Rv3811	-0.336	0.355
delta_Rv0954	0.376	-0.083
PonA1	0.893	-0.751
EccD1_KO	0.27	0.474
EspI_KO	-0.573	-0.622
PE35_KO	-0.038	0.175
PPE68_KO	0.243	-0.09
glycerol2	0.157	0.233
lignocerate	0.432	0.304
oleate	0.129	-0.238
phosphatidylcholine	0.345	-0.05
acetate	-0.203	0.141
glucAc	0.012	0.311
Rv0950ko	0.133	0.19
Rv1096ko	0.35	-0.033
Rv3684ko	-0.92	-0.684
delta_otsA_trehalose	0.054	-0.217