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 Rv0577/TB27.3

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

	Rv3621c/PPE65	Rv0577/TB27.3
Fe_supp_jason_reseq	1.108	0.028
low_pH_jason_reseq	-0.261	-0.954
NO_jason_reseq	-0.139	-0.234
B6_jason_reseq	0.629	0.242
MHCII_jason_reseq	0.742	0.772
Isoniazid02	-0.019	-0.205
Rifampicin4	-0.141	-0.758
Ethambutol3	0.0	-0.388
Meropenem3	1.579	2.391
Vancomycin16	0.199	-0.814
Rv2680_day32	0.526	0.888
H37Rv_KO_MarP	0.044	-0.073
hypoxia_3wks	0.024	0.231
hypoxia_6wks	-0.173	0.507
glycerol	0.221	-1.328
cholesterol	-0.431	-0.523
AJ	0.405	-0.311
Bibs02	0.261	0.052
Bibs02c	-0.246	-0.28
BL6	0.188	-0.564
BL6a	-0.172	0.063
BXD01	0.18	-0.157
BXD010	-0.825	-0.462
BXD011	1.466	1.074
BXD03	0.262	-0.496
BXD04	0.245	-0.581
BXD05	-0.237	-0.684
BXD06	-0.102	-0.343
BXD07	0.263	-0.117
BXD08	0.475	0.197
BXD09	0.188	0.12
CAST	0.252	-0.105
CCcont	0.301	-0.423
DS01	-0.145	0.075
DS02	-0.233	0.203
DS04	0.628	-0.164
DS0c	-0.189	-0.233
GP01	-0.032	-0.208
GP02	1.109	0.523
GP0c	0.366	0.164
NOD	0.918	0.098
NZO	0.965	-0.259
PWK	0.601	0.198
H37Rv_KO_CtpC	0.289	0.539
H37Rv_KO_CtpD	-0.041	-0.767
H37Rv_KO_Rv1272	0.403	0.29
H37Rv_KO_SugABC	0.426	0.703
H37Rv_KO_MbtN	0.723	0.104
Trans05	1.268	0.027
macrophage_unactivated	0.312	-0.448
IL1	-0.697	-0.7
Rapamycin	0.018	-0.767
Tcell	0.062	-0.257
GMCSF	0.306	0.314
IFNab	0.227	-0.865
IFNg	-0.158	0.123
IFNg_GMCSF1	0.808	-0.094
Rv1432_day32	-0.546	0.993
Rv1565c_day32	0.483	-0.673
secA2_input	0.282	1.224
delta_Rv3594	-0.179	-0.482
delta_Rv3717	-0.483	-0.171
delta_Rv3811	-0.103	-0.608
delta_Rv0954	-0.224	0.734
PonA1	0.328	0.606
EccD1_KO	0.875	1.243
EspI_KO	0.086	0.838
PE35_KO	0.557	1.21
PPE68_KO	0.467	0.253
glycerol2	0.667	0.419
lignocerate	0.665	0.479
oleate	0.469	0.469
phosphatidylcholine	0.577	0.237
acetate	0.168	0.0
glucAc	0.121	-0.129
Rv0950ko	0.956	0.021
Rv1096ko	0.642	1.013
Rv3684ko	0.717	0.829
delta_otsA_trehalose	-0.261	1.683