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 Rv2853/PE_PGRS48:

update plot	correlation	link to info on gene
Rv2352c/PPE38	(cc=0.5372)	info on Rv2352c/PPE38
Rv3223c/sigH	(cc=0.5123)	info on Rv3223c/sigH
Rv3045/adhC	(cc=0.512)	info on Rv3045/adhC
Rv0940c/-	(cc=0.5046)	info on Rv0940c/-
Rv3142c/-	(cc=0.4999)	info on Rv3142c/-
Rv0072/-	(cc=0.4958)	info on Rv0072/-
Rv0160c/PE4	(cc=0.4773)	info on Rv0160c/PE4
Rv3814c/-	(cc=0.4734)	info on Rv3814c/-
Rv3397c/phyA	(cc=0.464)	info on Rv3397c/phyA
Rv1498c/-	(cc=0.4635)	info on Rv1498c/-

Correlation of Rv2853/PE_PGRS48 with Rv3223c/sigH

Normalized LFCs for Rv2853/PE_PGRS48:
(description and provenance of datasets)

	Rv2853/PE_PGRS48	Rv3223c/sigH
Fe_supp_jason_reseq	0.641	1.377
low_pH_jason_reseq	-0.269	-1.166
NO_jason_reseq	0.06	-1.011
B6_jason_reseq	-0.414	-1.144
MHCII_jason_reseq	-0.425	-0.3
Isoniazid02	-0.965	-0.799
Rifampicin4	0.095	-0.333
Ethambutol3	0.258	1.049
Meropenem3	-1.22	-0.879
Vancomycin16	-0.788	-0.432
Rv2680_day32	-0.666	-1.414
H37Rv_KO_MarP	-0.206	-0.024
hypoxia_3wks	-0.335	-1.782
hypoxia_6wks	-0.72	-2.817
glycerol	0.587	1.612
cholesterol	0.29	2.7
AJ	0.881	0.432
Bibs02	0.199	1.605
Bibs02c	0.273	1.106
BL6	0.488	0.969
BL6a	0.462	1.435
BXD01	0.269	0.96
BXD010	0.324	0.554
BXD011	0.519	0.712
BXD03	0.679	1.014
BXD04	0.39	0.426
BXD05	0.242	1.074
BXD06	0.507	0.554
BXD07	0.494	0.316
BXD08	0.497	0.857
BXD09	0.213	0.677
CAST	0.475	0.707
CCcont	0.574	2.402
DS01	0.24	1.021
DS02	-0.408	0.055
DS04	0.623	0.52
DS0c	0.0	2.11
GP01	-0.129	1.964
GP02	0.108	0.301
GP0c	-0.182	0.297
NOD	0.61	0.418
NZO	0.344	1.202
PWK	0.078	-0.509
H37Rv_KO_CtpC	0.235	1.047
H37Rv_KO_CtpD	0.174	1.055
H37Rv_KO_Rv1272	0.811	2.343
H37Rv_KO_SugABC	-0.084	1.068
H37Rv_KO_MbtN	0.659	2.627
Trans05	1.389	2.3
macrophage_unactivated	-0.262	0.237
IL1	-0.196	-3.45
Rapamycin	-0.227	-1.715
Tcell	-0.381	-1.352
GMCSF	-0.404	-0.51
IFNab	-0.435	0.65
IFNg	-0.043	-2.405
IFNg_GMCSF1	-0.182	-1.197
Rv1432_day32	-0.018	-0.645
Rv1565c_day32	1.512	0.317
secA2_input	-0.747	-1.633
delta_Rv3594	-0.017	1.975
delta_Rv3717	0.169	0.896
delta_Rv3811	0.271	1.619
delta_Rv0954	-0.42	0.833
PonA1	0.667	-0.444
EccD1_KO	0.0	0.444
EspI_KO	0.493	0.197
PE35_KO	0.175	0.925
PPE68_KO	-0.134	1.075
glycerol2	-0.078	0.68
lignocerate	0.444	0.983
oleate	-0.016	0.822
phosphatidylcholine	0.245	1.21
acetate	0.053	0.457
glucAc	0.15	0.374
Rv0950ko	0.283	-0.06
Rv1096ko	0.654	-0.516
Rv3684ko	0.845	-0.711
delta_otsA_trehalose	0.127	2.183