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 Rv1112/-:

update plot	correlation	link to info on gene
Rv3269/-	(cc=0.6543)	info on Rv3269/-
Rv1008/tatD	(cc=0.6147)	info on Rv1008/tatD
Rv1170/mshB	(cc=0.6083)	info on Rv1170/mshB
Rv3624c/hpt	(cc=0.5741)	info on Rv3624c/hpt
Rv3755c/-	(cc=0.5657)	info on Rv3755c/-
Rv0819/mshD	(cc=0.558)	info on Rv0819/mshD
Rv2131c/cysQ	(cc=0.5561)	info on Rv2131c/cysQ
Rv2404c/lepA	(cc=0.5434)	info on Rv2404c/lepA
Rv1908c/katG	(cc=0.5319)	info on Rv1908c/katG
Rv3715c/recR	(cc=0.53)	info on Rv3715c/recR

Correlation of Rv1112/- with Rv3624c/hpt

Normalized LFCs for Rv1112/-:
(description and provenance of datasets)

	Rv1112/-	Rv3624c/hpt
Fe_supp_jason_reseq	1.901	0.218
low_pH_jason_reseq	-1.571	0.0
NO_jason_reseq	0.315	0.0
B6_jason_reseq	-0.913	0.0
MHCII_jason_reseq	0.0	0.0
Isoniazid02	3.87	2.043
Rifampicin4	0.712	0.433
Ethambutol3	1.414	0.285
Meropenem3	0.426	-0.335
Vancomycin16	1.602	0.218
Rv2680_day32	0.109	0.0
H37Rv_KO_MarP	2.428	0.35
hypoxia_3wks	-2.68	-0.885
hypoxia_6wks	-2.533	-0.727
glycerol	2.487	1.121
cholesterol	1.62	2.098
AJ	1.78	0.983
Bibs02	0.0	0.183
Bibs02c	0.0	0.0
BL6	1.574	0.238
BL6a	1.964	0.198
BXD01	1.496	0.64
BXD010	1.739	0.0
BXD011	0.612	0.0
BXD03	1.146	0.135
BXD04	1.588	0.607
BXD05	1.241	0.0
BXD06	2.098	0.254
BXD07	0.809	0.264
BXD08	1.227	0.0
BXD09	2.005	0.386
CAST	1.458	0.439
CCcont	4.277	1.231
DS01	0.551	0.83
DS02	0.35	0.0
DS04	1.32	0.194
DS0c	0.652	0.596
GP01	0.36	0.0
GP02	-0.159	0.0
GP0c	-0.248	0.0
NOD	2.071	0.0
NZO	1.357	0.0
PWK	0.715	0.0
H37Rv_KO_CtpC	0.0	0.0
H37Rv_KO_CtpD	1.689	0.0
H37Rv_KO_Rv1272	0.753	0.141
H37Rv_KO_SugABC	1.666	0.099
H37Rv_KO_MbtN	1.959	0.0
Trans05	0.628	0.131
macrophage_unactivated	0.571	0.0
IL1	-1.326	-0.409
Rapamycin	-0.307	-0.424
Tcell	0.303	-0.45
GMCSF	-0.85	0.0
IFNab	0.795	-0.417
IFNg	-1.563	-0.369
IFNg_GMCSF1	-0.647	-0.434
Rv1432_day32	1.155	0.0
Rv1565c_day32	-0.256	0.0
secA2_input	-0.676	-1.133
delta_Rv3594	4.577	1.127
delta_Rv3717	4.406	-0.405
delta_Rv3811	3.248	-0.306
delta_Rv0954	0.969	1.526
PonA1	-0.245	0.394
EccD1_KO	-1.542	-1.365
EspI_KO	-1.879	-2.053
PE35_KO	-0.548	-0.475
PPE68_KO	-0.902	-0.342
glycerol2	0.395	-1.876
lignocerate	-0.764	-1.736
oleate	-0.588	-1.67
phosphatidylcholine	-1.751	-2.578
acetate	1.536	-0.635
glucAc	2.08	-0.808
Rv0950ko	0.862	0.639
Rv1096ko	0.398	0.832
Rv3684ko	0.829	0.0
delta_otsA_trehalose	0.4	0.0