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 Rv0968/-:

update plot	correlation	link to info on gene
Rv0342/iniA	(cc=0.6427)	info on Rv0342/iniA
Rv3472/-	(cc=0.6354)	info on Rv3472/-
Rv3312c/-	(cc=0.6277)	info on Rv3312c/-
Rv0399c/lpqK	(cc=0.6234)	info on Rv0399c/lpqK
Rv1997/ctpF	(cc=0.6072)	info on Rv1997/ctpF
Rv3566c/nat	(cc=0.6067)	info on Rv3566c/nat
Rv3447c/eccC4	(cc=0.5768)	info on Rv3447c/eccC4
Rv3162c/-	(cc=0.5573)	info on Rv3162c/-
Rv2313c/-	(cc=0.5542)	info on Rv2313c/-
Rv2679/echA15	(cc=0.5541)	info on Rv2679/echA15

Correlation of Rv0968/- with Rv0399c/lpqK

Normalized LFCs for Rv0968/-:
(description and provenance of datasets)

	Rv0968/-	Rv0399c/lpqK
Fe_supp_jason_reseq	0.704	0.215
low_pH_jason_reseq	-0.738	0.087
NO_jason_reseq	0.423	0.522
B6_jason_reseq	0.01	0.114
MHCII_jason_reseq	0.27	0.21
Isoniazid02	-3.296	-3.51
Rifampicin4	0.831	0.764
Ethambutol3	-2.914	-2.908
Meropenem3	-3.018	-2.207
Vancomycin16	-1.112	-1.08
Rv2680_day32	0.91	-0.648
H37Rv_KO_MarP	0.883	-0.277
hypoxia_3wks	-0.203	0.375
hypoxia_6wks	-1.349	1.054
glycerol	0.677	0.107
cholesterol	0.845	0.349
AJ	0.528	0.153
Bibs02	-0.278	-0.076
Bibs02c	0.671	1.291
BL6	-0.789	-0.052
BL6a	-0.393	0.936
BXD01	-0.379	0.069
BXD010	-0.019	0.39
BXD011	-0.923	-0.185
BXD03	-0.794	0.695
BXD04	-0.426	0.244
BXD05	0.48	0.488
BXD06	-0.954	0.018
BXD07	-0.699	0.091
BXD08	-0.379	0.444
BXD09	-0.542	0.0
CAST	0.265	0.062
CCcont	-0.929	-0.127
DS01	-0.469	0.544
DS02	0.635	-0.121
DS04	0.093	0.966
DS0c	-0.211	0.523
GP01	0.345	-0.144
GP02	-0.744	-0.527
GP0c	-0.329	0.018
NOD	0.885	1.193
NZO	-0.27	-0.027
PWK	-0.254	0.129
H37Rv_KO_CtpC	-0.14	0.086
H37Rv_KO_CtpD	1.622	1.419
H37Rv_KO_Rv1272	1.062	-0.079
H37Rv_KO_SugABC	0.86	0.683
H37Rv_KO_MbtN	-1.047	0.215
Trans05	-0.921	0.052
macrophage_unactivated	-0.843	-0.363
IL1	-0.946	-0.78
Rapamycin	-1.105	0.381
Tcell	-0.472	0.176
GMCSF	-0.055	0.327
IFNab	-0.13	-0.662
IFNg	-0.516	-0.051
IFNg_GMCSF1	-0.569	0.443
Rv1432_day32	-0.215	0.082
Rv1565c_day32	0.445	0.269
secA2_input	1.842	0.312
delta_Rv3594	0.096	0.057
delta_Rv3717	-0.593	0.115
delta_Rv3811	-0.167	-0.028
delta_Rv0954	-0.105	-0.96
PonA1	1.324	-0.112
EccD1_KO	1.237	0.161
EspI_KO	-0.074	0.274
PE35_KO	0.111	0.236
PPE68_KO	-0.192	0.259
glycerol2	0.146	0.238
lignocerate	0.072	0.524
oleate	0.18	0.631
phosphatidylcholine	0.326	0.496
acetate	0.352	0.535
glucAc	0.061	0.349
Rv0950ko	0.458	0.048
Rv1096ko	1.2	0.745
Rv3684ko	0.652	-0.321
delta_otsA_trehalose	1.843	0.178