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 Rv1709/scpA:

update plot	correlation	link to info on gene
Rv2922c/smc	(cc=0.5607)	info on Rv2922c/smc
Rv0892/-	(cc=0.5404)	info on Rv0892/-
Rv2807/-	(cc=0.5379)	info on Rv2807/-
Rv2169c/-	(cc=0.5243)	info on Rv2169c/-
Rv3187/-	(cc=0.5242)	info on Rv3187/-
Rv2167c/-	(cc=0.5196)	info on Rv2167c/-
Rv1756c/-	(cc=0.5173)	info on Rv1756c/-
Rv2428/ahpC	(cc=0.5127)	info on Rv2428/ahpC
Rv3023c/-	(cc=0.5039)	info on Rv3023c/-
Rv1047/-	(cc=0.5027)	info on Rv1047/-

Correlation of Rv1709/scpA with Rv2922c/smc

Normalized LFCs for Rv1709/scpA:
(description and provenance of datasets)

	Rv1709/scpA	Rv2922c/smc
Fe_supp_jason_reseq	-0.865	0.33
low_pH_jason_reseq	-0.718	0.44
NO_jason_reseq	1.019	0.244
B6_jason_reseq	0.047	-1.074
MHCII_jason_reseq	-0.021	-0.131
Isoniazid02	-1.224	-0.706
Rifampicin4	-0.544	0.079
Ethambutol3	-1.285	-0.4
Meropenem3	0.486	0.231
Vancomycin16	-2.141	-1.512
Rv2680_day32	-0.462	-1.31
H37Rv_KO_MarP	-0.696	-0.737
hypoxia_3wks	-0.542	-0.475
hypoxia_6wks	0.067	-0.426
glycerol	-0.484	0.876
cholesterol	0.426	0.96
AJ	0.499	0.069
Bibs02	-0.22	1.431
Bibs02c	1.047	0.823
BL6	0.693	1.235
BL6a	1.28	0.654
BXD01	0.546	0.28
BXD010	1.171	0.849
BXD011	0.657	0.578
BXD03	0.176	0.738
BXD04	0.739	1.696
BXD05	0.641	0.256
BXD06	0.844	0.552
BXD07	0.484	0.545
BXD08	0.592	0.15
BXD09	0.703	0.268
CAST	0.085	-0.452
CCcont	0.055	1.059
DS01	0.604	1.331
DS02	-0.055	0.944
DS04	0.398	0.554
DS0c	1.281	1.332
GP01	0.252	-0.433
GP02	-0.572	0.159
GP0c	0.239	-0.631
NOD	0.164	0.13
NZO	-1.016	-1.166
PWK	1.101	0.56
H37Rv_KO_CtpC	1.333	2.049
H37Rv_KO_CtpD	1.511	0.39
H37Rv_KO_Rv1272	0.592	0.979
H37Rv_KO_SugABC	-0.302	0.057
H37Rv_KO_MbtN	-0.814	0.792
Trans05	0.905	0.402
macrophage_unactivated	-0.691	0.48
IL1	-0.24	-0.196
Rapamycin	-1.007	-0.203
Tcell	-0.505	-0.326
GMCSF	0.528	0.478
IFNab	-0.741	0.877
IFNg	0.176	0.329
IFNg_GMCSF1	-1.119	0.386
Rv1432_day32	-1.64	-0.085
Rv1565c_day32	1.041	0.21
secA2_input	0.366	0.568
delta_Rv3594	-0.268	0.532
delta_Rv3717	0.44	0.159
delta_Rv3811	-0.135	0.039
delta_Rv0954	-1.833	-1.258
PonA1	0.443	-0.335
EccD1_KO	1.01	-1.154
EspI_KO	1.928	-0.171
PE35_KO	0.753	-0.744
PPE68_KO	0.454	-0.528
glycerol2	-1.681	-1.529
lignocerate	-2.151	-1.967
oleate	-1.701	-1.638
phosphatidylcholine	-2.105	-2.024
acetate	-1.132	-0.258
glucAc	-1.767	-0.732
Rv0950ko	-0.368	-0.859
Rv1096ko	1.013	0.314
Rv3684ko	0.789	-0.521
delta_otsA_trehalose	-1.327	0.346