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 Rv3293/pcd:

update plot	correlation	link to info on gene
Rv2062c/cobN	(cc=0.4643)	info on Rv2062c/cobN
Rv0488/-	(cc=0.4558)	info on Rv0488/-
Rv0906/-	(cc=0.432)	info on Rv0906/-
Rv3600c/-	(cc=0.4256)	info on Rv3600c/-
Rv2260/-	(cc=0.4095)	info on Rv2260/-
Rv0399c/lpqK	(cc=0.406)	info on Rv0399c/lpqK
Rv1997/ctpF	(cc=0.4035)	info on Rv1997/ctpF
Rv0269c/-	(cc=0.4027)	info on Rv0269c/-
Rv3191c/-	(cc=0.4001)	info on Rv3191c/-
Rv3175/-	(cc=0.3983)	info on Rv3175/-

Correlation of Rv3293/pcd with Rv0269c/-

Normalized LFCs for Rv3293/pcd:
(description and provenance of datasets)

	Rv3293/pcd	Rv0269c/-
Fe_supp_jason_reseq	-0.624	0.905
low_pH_jason_reseq	0.216	-0.099
NO_jason_reseq	0.339	0.029
B6_jason_reseq	1.237	1.569
MHCII_jason_reseq	0.486	1.229
Isoniazid02	-1.072	0.012
Rifampicin4	0.024	0.333
Ethambutol3	-0.989	0.295
Meropenem3	-0.474	0.054
Vancomycin16	-0.531	-0.082
Rv2680_day32	0.49	1.037
H37Rv_KO_MarP	-0.363	0.574
hypoxia_3wks	-1.037	0.199
hypoxia_6wks	-0.52	0.248
glycerol	-0.607	-0.313
cholesterol	-0.222	0.086
AJ	-0.118	0.148
Bibs02	0.511	-0.293
Bibs02c	0.859	0.192
BL6	-0.66	-0.227
BL6a	0.178	0.0
BXD01	-0.052	0.006
BXD010	-0.038	-0.161
BXD011	-0.682	-0.453
BXD03	-0.033	-0.223
BXD04	-0.397	0.083
BXD05	-0.294	-0.513
BXD06	0.033	0.057
BXD07	-0.099	-0.201
BXD08	0.0	0.44
BXD09	-0.508	-0.102
CAST	0.185	-0.03
CCcont	-0.429	-0.286
DS01	0.849	0.373
DS02	0.356	0.767
DS04	0.156	0.025
DS0c	-0.284	0.8
GP01	-0.24	1.082
GP02	-0.586	-0.014
GP0c	0.146	0.349
NOD	-0.69	-0.679
NZO	-1.169	0.231
PWK	-0.602	0.06
H37Rv_KO_CtpC	0.448	-0.111
H37Rv_KO_CtpD	0.537	1.228
H37Rv_KO_Rv1272	-0.274	-0.248
H37Rv_KO_SugABC	0.239	-0.687
H37Rv_KO_MbtN	0.252	0.087
Trans05	0.112	0.575
macrophage_unactivated	-0.234	-0.423
IL1	-0.11	-0.522
Rapamycin	0.163	0.068
Tcell	-0.56	0.098
GMCSF	0.116	0.0
IFNab	-0.224	-0.405
IFNg	-0.516	-0.38
IFNg_GMCSF1	0.085	1.125
Rv1432_day32	0.945	0.209
Rv1565c_day32	0.542	0.957
secA2_input	0.014	0.16
delta_Rv3594	-0.806	-0.462
delta_Rv3717	0.093	-0.773
delta_Rv3811	-0.813	-1.453
delta_Rv0954	-0.669	-0.474
PonA1	-0.563	0.38
EccD1_KO	0.178	0.355
EspI_KO	0.605	-0.143
PE35_KO	-0.053	0.198
PPE68_KO	-0.147	-0.16
glycerol2	-0.286	0.242
lignocerate	0.0	0.413
oleate	-0.147	0.671
phosphatidylcholine	-0.097	0.367
acetate	0.69	0.221
glucAc	0.601	0.302
Rv0950ko	0.392	0.259
Rv1096ko	1.493	0.739
Rv3684ko	0.357	0.629
delta_otsA_trehalose	-0.461	0.272