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 Rv2544/lppB:

update plot	correlation	link to info on gene
Rv1987/-	(cc=0.7003)	info on Rv1987/-
Rv1471/trxB1	(cc=0.6987)	info on Rv1471/trxB1
Rv3528c/-	(cc=0.6054)	info on Rv3528c/-
Rv3232c/ppk2	(cc=0.5719)	info on Rv3232c/ppk2
Rv1499/-	(cc=0.5647)	info on Rv1499/-
Rv0997/-	(cc=0.5621)	info on Rv0997/-
Rv1896c/-	(cc=0.5584)	info on Rv1896c/-
Rv3148/nuoD	(cc=0.5548)	info on Rv3148/nuoD
Rv1502/-	(cc=0.5534)	info on Rv1502/-
Rv1548c/PPE21	(cc=0.5495)	info on Rv1548c/PPE21

Correlation of Rv2544/lppB with Rv1987/-

Normalized LFCs for Rv2544/lppB:
(description and provenance of datasets)

	Rv2544/lppB	Rv1987/-
Fe_supp_jason_reseq	1.127	0.813
low_pH_jason_reseq	-1.017	-0.965
NO_jason_reseq	0.173	-0.761
B6_jason_reseq	0.024	0.082
MHCII_jason_reseq	-1.788	-0.367
Isoniazid02	0.0	-0.346
Rifampicin4	-0.883	-0.709
Ethambutol3	-0.353	-0.343
Meropenem3	-0.391	-0.765
Vancomycin16	0.799	-0.053
Rv2680_day32	0.305	0.985
H37Rv_KO_MarP	-0.246	-0.008
hypoxia_3wks	-0.813	-1.025
hypoxia_6wks	-0.115	-0.265
glycerol	0.06	-0.933
cholesterol	-0.184	-0.517
AJ	-0.071	-0.679
Bibs02	0.437	0.878
Bibs02c	1.105	0.697
BL6	1.373	0.885
BL6a	1.738	0.422
BXD01	1.583	0.19
BXD010	1.615	0.059
BXD011	1.618	0.262
BXD03	1.844	0.478
BXD04	1.957	0.068
BXD05	1.846	0.698
BXD06	1.135	0.355
BXD07	1.284	0.167
BXD08	1.041	0.438
BXD09	1.435	0.363
CAST	-0.908	-0.289
CCcont	1.744	1.188
DS01	0.137	0.183
DS02	-0.276	-0.072
DS04	0.554	0.572
DS0c	-0.275	-0.083
GP01	-0.745	0.187
GP02	-0.444	-0.69
GP0c	-0.83	-0.935
NOD	-0.361	-0.295
NZO	-0.253	-0.767
PWK	1.172	-0.163
H37Rv_KO_CtpC	2.292	0.154
H37Rv_KO_CtpD	1.467	1.731
H37Rv_KO_Rv1272	1.852	0.848
H37Rv_KO_SugABC	1.493	1.386
H37Rv_KO_MbtN	2.949	-0.315
Trans05	1.969	0.03
macrophage_unactivated	0.249	0.265
IL1	0.178	0.409
Rapamycin	0.061	0.69
Tcell	0.56	-0.541
GMCSF	0.309	0.393
IFNab	0.296	0.242
IFNg	0.828	0.398
IFNg_GMCSF1	1.901	0.795
Rv1432_day32	0.035	0.194
Rv1565c_day32	1.311	0.117
secA2_input	-0.606	-0.418
delta_Rv3594	1.201	1.086
delta_Rv3717	0.055	0.703
delta_Rv3811	0.86	0.747
delta_Rv0954	0.727	1.417
PonA1	0.075	-0.212
EccD1_KO	0.059	-0.615
EspI_KO	0.485	-0.331
PE35_KO	0.855	-0.079
PPE68_KO	0.841	0.214
glycerol2	2.159	2.285
lignocerate	2.678	2.814
oleate	-1.239	-1.163
phosphatidylcholine	2.189	2.129
acetate	2.909	2.72
glucAc	2.554	2.553
Rv0950ko	0.121	0.033
Rv1096ko	-0.712	-0.549
Rv3684ko	-0.517	-0.416
delta_otsA_trehalose	-0.318	0.021