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 Rv3621c/PPE65:

update plot	correlation	link to info on gene
Rv1894c/-	(cc=0.4567)	info on Rv1894c/-
Rv3055/-	(cc=0.423)	info on Rv3055/-
Rv0577/TB27.3	(cc=0.4204)	info on Rv0577/TB27.3
Rv2079/-	(cc=0.4061)	info on Rv2079/-
Rv2025c/-	(cc=0.4017)	info on Rv2025c/-
Rv0962c/lprP	(cc=0.387)	info on Rv0962c/lprP
Rv1053c/-	(cc=0.3814)	info on Rv1053c/-
Rv1760/-	(cc=0.381)	info on Rv1760/-
Rv3595c/PE_PGRS59	(cc=0.3806)	info on Rv3595c/PE_PGRS59
Rv2755c/hsdS.1	(cc=0.3681)	info on Rv2755c/hsdS.1

Correlation of Rv3621c/PPE65 with Rv0962c/lprP

Normalized LFCs for Rv3621c/PPE65:
(description and provenance of datasets)

	Rv3621c/PPE65	Rv0962c/lprP
Fe_supp_jason_reseq	1.108	-0.287
low_pH_jason_reseq	-0.261	-0.415
NO_jason_reseq	-0.139	-0.627
B6_jason_reseq	0.629	0.751
MHCII_jason_reseq	0.742	0.417
Isoniazid02	-0.019	-0.012
Rifampicin4	-0.141	-0.271
Ethambutol3	0.0	0.123
Meropenem3	1.579	1.128
Vancomycin16	0.199	0.042
Rv2680_day32	0.526	0.903
H37Rv_KO_MarP	0.044	-0.231
hypoxia_3wks	0.024	0.423
hypoxia_6wks	-0.173	0.065
glycerol	0.221	-1.078
cholesterol	-0.431	-0.866
AJ	0.405	0.106
Bibs02	0.261	-0.416
Bibs02c	-0.246	-0.732
BL6	0.188	0.3
BL6a	-0.172	-0.719
BXD01	0.18	-0.281
BXD010	-0.825	-0.199
BXD011	1.466	-0.19
BXD03	0.262	-0.455
BXD04	0.245	0.611
BXD05	-0.237	0.313
BXD06	-0.102	-0.006
BXD07	0.263	-0.185
BXD08	0.475	-0.257
BXD09	0.188	-0.24
CAST	0.252	-0.177
CCcont	0.301	-0.612
DS01	-0.145	0.022
DS02	-0.233	0.156
DS04	0.628	-0.149
DS0c	-0.189	-0.583
GP01	-0.032	0.604
GP02	1.109	1.462
GP0c	0.366	1.069
NOD	0.918	-0.348
NZO	0.965	0.277
PWK	0.601	0.412
H37Rv_KO_CtpC	0.289	0.131
H37Rv_KO_CtpD	-0.041	0.261
H37Rv_KO_Rv1272	0.403	0.013
H37Rv_KO_SugABC	0.426	0.54
H37Rv_KO_MbtN	0.723	-0.176
Trans05	1.268	0.74
macrophage_unactivated	0.312	0.028
IL1	-0.697	-0.516
Rapamycin	0.018	-0.273
Tcell	0.062	0.0
GMCSF	0.306	0.201
IFNab	0.227	-0.411
IFNg	-0.158	0.224
IFNg_GMCSF1	0.808	0.107
Rv1432_day32	-0.546	0.278
Rv1565c_day32	0.483	0.711
secA2_input	0.282	0.204
delta_Rv3594	-0.179	0.217
delta_Rv3717	-0.483	0.299
delta_Rv3811	-0.103	-0.059
delta_Rv0954	-0.224	-0.066
PonA1	0.328	0.012
EccD1_KO	0.875	0.701
EspI_KO	0.086	0.071
PE35_KO	0.557	0.169
PPE68_KO	0.467	-0.054
glycerol2	0.667	-0.071
lignocerate	0.665	-0.072
oleate	0.469	0.322
phosphatidylcholine	0.577	0.08
acetate	0.168	-0.073
glucAc	0.121	-0.251
Rv0950ko	0.956	-0.133
Rv1096ko	0.642	0.546
Rv3684ko	0.717	-0.118
delta_otsA_trehalose	-0.261	-0.108