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 Rv1008/tatD

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

	Rv1112/-	Rv1008/tatD
Fe_supp_jason_reseq	1.901	1.02
low_pH_jason_reseq	-1.571	-0.765
NO_jason_reseq	0.315	0.643
B6_jason_reseq	-0.913	0.745
MHCII_jason_reseq	0.0	-0.534
Isoniazid02	3.87	1.227
Rifampicin4	0.712	0.292
Ethambutol3	1.414	0.293
Meropenem3	0.426	0.915
Vancomycin16	1.602	0.034
Rv2680_day32	0.109	1.397
H37Rv_KO_MarP	2.428	-0.487
hypoxia_3wks	-2.68	-0.443
hypoxia_6wks	-2.533	0.109
glycerol	2.487	1.745
cholesterol	1.62	0.762
AJ	1.78	0.121
Bibs02	0.0	-0.115
Bibs02c	0.0	0.017
BL6	1.574	0.352
BL6a	1.964	0.788
BXD01	1.496	0.229
BXD010	1.739	0.932
BXD011	0.612	0.553
BXD03	1.146	0.737
BXD04	1.588	1.43
BXD05	1.241	0.463
BXD06	2.098	1.202
BXD07	0.809	0.529
BXD08	1.227	0.351
BXD09	2.005	0.552
CAST	1.458	-0.108
CCcont	4.277	1.407
DS01	0.551	0.678
DS02	0.35	0.082
DS04	1.32	1.251
DS0c	0.652	0.558
GP01	0.36	0.377
GP02	-0.159	-0.209
GP0c	-0.248	0.822
NOD	2.071	0.133
NZO	1.357	-0.03
PWK	0.715	0.77
H37Rv_KO_CtpC	0.0	-0.255
H37Rv_KO_CtpD	1.689	0.684
H37Rv_KO_Rv1272	0.753	0.626
H37Rv_KO_SugABC	1.666	0.954
H37Rv_KO_MbtN	1.959	1.652
Trans05	0.628	0.526
macrophage_unactivated	0.571	0.082
IL1	-1.326	-1.608
Rapamycin	-0.307	-0.537
Tcell	0.303	-0.261
GMCSF	-0.85	-0.903
IFNab	0.795	0.305
IFNg	-1.563	-1.125
IFNg_GMCSF1	-0.647	-1.005
Rv1432_day32	1.155	1.212
Rv1565c_day32	-0.256	0.141
secA2_input	-0.676	0.18
delta_Rv3594	4.577	0.928
delta_Rv3717	4.406	1.202
delta_Rv3811	3.248	0.605
delta_Rv0954	0.969	-0.645
PonA1	-0.245	-0.122
EccD1_KO	-1.542	0.079
EspI_KO	-1.879	-0.328
PE35_KO	-0.548	0.07
PPE68_KO	-0.902	-0.262
glycerol2	0.395	0.516
lignocerate	-0.764	-0.011
oleate	-0.588	0.099
phosphatidylcholine	-1.751	-0.296
acetate	1.536	0.923
glucAc	2.08	0.149
Rv0950ko	0.862	-0.033
Rv1096ko	0.398	0.452
Rv3684ko	0.829	0.344
delta_otsA_trehalose	0.4	-0.035