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 Rv1196/PPE18:

update plot	correlation	link to info on gene
Rv1194c/-	(cc=0.6576)	info on Rv1194c/-
Rv1195/PE13	(cc=0.6444)	info on Rv1195/PE13
Rv1872c/lldD2	(cc=0.5814)	info on Rv1872c/lldD2
Rv3223c/sigH	(cc=0.5787)	info on Rv3223c/sigH
Rv1364c/-	(cc=0.5578)	info on Rv1364c/-
Rv3152/nuoH	(cc=0.5339)	info on Rv3152/nuoH
Rv2107/PE22	(cc=0.5322)	info on Rv2107/PE22
Rv2814c/-	(cc=0.5308)	info on Rv2814c/-
Rv2479c/-	(cc=0.5303)	info on Rv2479c/-
Rv2106/-	(cc=0.5263)	info on Rv2106/-

Correlation of Rv1196/PPE18 with Rv1194c/-

Normalized LFCs for Rv1196/PPE18:
(description and provenance of datasets)

	Rv1196/PPE18	Rv1194c/-
Fe_supp_jason_reseq	-0.06	-0.549
low_pH_jason_reseq	-1.091	0.231
NO_jason_reseq	-0.914	-1.759
B6_jason_reseq	-1.217	-0.604
MHCII_jason_reseq	0.228	0.829
Isoniazid02	2.462	0.26
Rifampicin4	0.842	0.558
Ethambutol3	1.445	-0.339
Meropenem3	-0.121	-0.503
Vancomycin16	0.531	0.244
Rv2680_day32	-1.276	-0.333
H37Rv_KO_MarP	-0.934	-0.387
hypoxia_3wks	0.626	0.243
hypoxia_6wks	0.875	0.065
glycerol	0.828	1.906
cholesterol	0.379	1.25
AJ	1.657	1.062
Bibs02	0.685	0.775
Bibs02c	1.155	0.517
BL6	1.282	0.99
BL6a	1.591	0.595
BXD01	0.97	-0.169
BXD010	0.644	-0.117
BXD011	1.367	0.416
BXD03	1.557	0.804
BXD04	0.999	0.796
BXD05	1.494	0.69
BXD06	0.919	0.33
BXD07	0.923	0.159
BXD08	1.004	0.023
BXD09	1.004	0.943
CAST	0.863	-0.082
CCcont	1.275	0.888
DS01	1.246	1.983
DS02	0.892	0.844
DS04	1.684	1.456
DS0c	1.171	1.609
GP01	0.765	0.918
GP02	0.418	0.261
GP0c	0.506	0.321
NOD	0.133	0.428
NZO	0.761	1.043
PWK	0.999	1.067
H37Rv_KO_CtpC	-0.175	-1.294
H37Rv_KO_CtpD	1.298	0.278
H37Rv_KO_Rv1272	1.113	1.561
H37Rv_KO_SugABC	1.499	1.002
H37Rv_KO_MbtN	1.065	0.135
Trans05	0.993	0.628
macrophage_unactivated	0.246	0.347
IL1	-1.16	-1.447
Rapamycin	-0.35	-0.043
Tcell	-1.0	-2.294
GMCSF	-0.742	-0.396
IFNab	1.62	1.608
IFNg	-1.868	-0.711
IFNg_GMCSF1	-0.308	-0.782
Rv1432_day32	-0.271	-0.24
Rv1565c_day32	-0.101	0.438
secA2_input	-0.312	0.28
delta_Rv3594	0.569	0.254
delta_Rv3717	0.865	-0.508
delta_Rv3811	0.758	0.07
delta_Rv0954	0.339	-0.578
PonA1	-0.369	0.09
EccD1_KO	0.122	0.408
EspI_KO	1.32	1.184
PE35_KO	0.72	0.785
PPE68_KO	0.157	0.118
glycerol2	1.103	0.535
lignocerate	0.742	-0.356
oleate	-0.425	-1.474
phosphatidylcholine	1.064	0.31
acetate	-0.045	-0.712
glucAc	0.176	-0.865
Rv0950ko	-0.057	0.0
Rv1096ko	-0.03	0.296
Rv3684ko	-0.226	-0.144
delta_otsA_trehalose	1.263	0.759