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 Rv3138/pflA:

update plot	correlation	link to info on gene
Rv2998/-	(cc=0.5123)	info on Rv2998/-
Rv0905/echA6	(cc=0.4915)	info on Rv0905/echA6
Rv0397A/-	(cc=0.4896)	info on Rv0397A/-
Rv0365c/-	(cc=0.4881)	info on Rv0365c/-
Rv1525/wbbL2	(cc=0.4791)	info on Rv1525/wbbL2
Rv3126c/-	(cc=0.4715)	info on Rv3126c/-
Rv3529c/-	(cc=0.4674)	info on Rv3529c/-
Rv0605/-	(cc=0.4519)	info on Rv0605/-
Rv0845/-	(cc=0.4493)	info on Rv0845/-
Rv2634c/PE_PGRS46	(cc=0.4489)	info on Rv2634c/PE_PGRS46

Correlation of Rv3138/pflA with Rv2998/-

Normalized LFCs for Rv3138/pflA:
(description and provenance of datasets)

	Rv3138/pflA	Rv2998/-
Fe_supp_jason_reseq	-0.298	0.0
low_pH_jason_reseq	0.089	-1.074
NO_jason_reseq	-0.06	0.378
B6_jason_reseq	-0.658	-0.74
MHCII_jason_reseq	-0.094	0.621
Isoniazid02	0.153	-0.723
Rifampicin4	-0.173	0.647
Ethambutol3	0.358	-0.373
Meropenem3	-0.818	-1.329
Vancomycin16	-0.485	-0.568
Rv2680_day32	-0.696	-2.766
H37Rv_KO_MarP	0.346	0.401
hypoxia_3wks	-0.032	0.044
hypoxia_6wks	-0.081	0.67
glycerol	-0.575	-0.357
cholesterol	0.068	-0.07
AJ	0.425	-0.015
Bibs02	0.527	-0.558
Bibs02c	0.582	0.571
BL6	0.17	0.368
BL6a	0.732	0.927
BXD01	0.703	0.66
BXD010	0.479	-0.018
BXD011	2.15	0.008
BXD03	0.39	0.289
BXD04	0.702	0.389
BXD05	0.833	1.214
BXD06	0.587	0.642
BXD07	0.831	0.769
BXD08	0.054	0.684
BXD09	0.746	0.576
CAST	-0.132	0.137
CCcont	0.454	-0.389
DS01	0.0	-0.536
DS02	0.269	-0.438
DS04	-0.571	-0.208
DS0c	0.36	1.571
GP01	0.456	1.334
GP02	0.077	-0.538
GP0c	-0.103	-0.23
NOD	-0.212	-0.174
NZO	0.678	-0.663
PWK	0.772	0.993
H37Rv_KO_CtpC	-0.241	0.613
H37Rv_KO_CtpD	-0.198	1.171
H37Rv_KO_Rv1272	0.362	0.714
H37Rv_KO_SugABC	-0.155	-1.841
H37Rv_KO_MbtN	-0.113	-1.256
Trans05	0.469	0.127
macrophage_unactivated	1.275	0.877
IL1	0.736	0.068
Rapamycin	0.292	0.071
Tcell	0.489	0.345
GMCSF	0.57	1.085
IFNab	0.133	0.121
IFNg	0.454	0.535
IFNg_GMCSF1	0.877	0.214
Rv1432_day32	0.159	1.7
Rv1565c_day32	0.224	-0.381
secA2_input	-0.366	-0.304
delta_Rv3594	-0.878	-2.168
delta_Rv3717	-0.943	-1.986
delta_Rv3811	-0.665	-1.698
delta_Rv0954	0.12	-1.265
PonA1	-0.459	-2.401
EccD1_KO	0.98	1.214
EspI_KO	0.268	0.633
PE35_KO	0.274	1.896
PPE68_KO	0.358	1.609
glycerol2	0.156	0.371
lignocerate	0.379	-0.186
oleate	0.021	0.74
phosphatidylcholine	0.328	0.577
acetate	-0.286	-0.977
glucAc	-0.017	-1.121
Rv0950ko	0.28	0.757
Rv1096ko	0.13	1.707
Rv3684ko	0.616	-0.242
delta_otsA_trehalose	0.181	-2.389