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 Rv0124/PE_PGRS2:

update plot	correlation	link to info on gene
Rv0620/galK	(cc=0.4403)	info on Rv0620/galK
Rv0094c/-	(cc=0.424)	info on Rv0094c/-
Rv0279c/PE_PGRS4	(cc=0.42)	info on Rv0279c/PE_PGRS4
Rv0578c/PE_PGRS7	(cc=0.4139)	info on Rv0578c/PE_PGRS7
Rv3467/-	(cc=0.4137)	info on Rv3467/-
Rv1091/PE_PGRS22	(cc=0.4132)	info on Rv1091/PE_PGRS22
Rv3345c/PE_PGRS50	(cc=0.4093)	info on Rv3345c/PE_PGRS50
Rv0393/-	(cc=0.4032)	info on Rv0393/-
Rv1818c/PE_PGRS33	(cc=0.4028)	info on Rv1818c/PE_PGRS33
Rv1468c/PE_PGRS29	(cc=0.4008)	info on Rv1468c/PE_PGRS29

Correlation of Rv0124/PE_PGRS2 with Rv3467/-

Normalized LFCs for Rv0124/PE_PGRS2:
(description and provenance of datasets)

	Rv0124/PE_PGRS2	Rv3467/-
Fe_supp_jason_reseq	-0.627	0.111
low_pH_jason_reseq	-0.284	0.202
NO_jason_reseq	-0.525	0.339
B6_jason_reseq	-0.542	0.125
MHCII_jason_reseq	-0.477	0.061
Isoniazid02	-0.535	0.391
Rifampicin4	0.671	0.352
Ethambutol3	1.019	0.561
Meropenem3	0.26	1.019
Vancomycin16	0.048	0.159
Rv2680_day32	-0.183	-0.448
H37Rv_KO_MarP	-0.109	-0.034
hypoxia_3wks	-0.407	-0.12
hypoxia_6wks	-1.155	-0.666
glycerol	0.674	-0.692
cholesterol	-0.4	-0.55
AJ	0.59	0.866
Bibs02	0.874	0.571
Bibs02c	0.239	0.732
BL6	-0.502	0.264
BL6a	-0.156	0.936
BXD01	1.066	0.144
BXD010	-0.764	0.74
BXD011	-0.232	0.126
BXD03	-0.107	0.751
BXD04	0.726	0.701
BXD05	0.55	0.305
BXD06	-0.478	0.209
BXD07	0.566	0.596
BXD08	0.459	0.274
BXD09	0.062	0.251
CAST	0.325	0.617
CCcont	0.15	-0.101
DS01	0.139	0.621
DS02	0.797	0.945
DS04	1.285	0.776
DS0c	-0.556	0.363
GP01	0.393	0.575
GP02	1.174	0.752
GP0c	0.682	0.604
NOD	0.132	-0.075
NZO	1.591	0.525
PWK	0.0	0.87
H37Rv_KO_CtpC	1.26	0.692
H37Rv_KO_CtpD	-0.657	0.04
H37Rv_KO_Rv1272	0.701	0.0
H37Rv_KO_SugABC	-1.391	-0.637
H37Rv_KO_MbtN	-0.369	-0.372
Trans05	0.0	0.691
macrophage_unactivated	-0.11	-1.016
IL1	-0.377	-0.122
Rapamycin	0.0	-0.227
Tcell	-0.87	-0.671
GMCSF	-0.092	-0.877
IFNab	-1.203	-1.004
IFNg	0.756	-0.337
IFNg_GMCSF1	-0.644	-0.233
Rv1432_day32	0.205	-0.143
Rv1565c_day32	0.036	0.377
secA2_input	1.393	0.338
delta_Rv3594	0.454	0.225
delta_Rv3717	0.03	-0.121
delta_Rv3811	0.158	0.104
delta_Rv0954	0.062	0.8
PonA1	1.196	0.126
EccD1_KO	-0.164	0.115
EspI_KO	-1.657	-0.051
PE35_KO	-0.939	-0.053
PPE68_KO	-0.413	-0.115
glycerol2	-0.128	-0.944
lignocerate	-0.055	-0.543
oleate	-0.043	-0.977
phosphatidylcholine	-0.41	-0.539
acetate	0.768	0.577
glucAc	0.117	0.321
Rv0950ko	0.766	-0.573
Rv1096ko	0.866	0.531
Rv3684ko	1.755	0.0
delta_otsA_trehalose	0.683	0.631