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 Rv3698/-:

update plot	correlation	link to info on gene
Rv2946c/pks1	(cc=0.4727)	info on Rv2946c/pks1
Rv1879/-	(cc=0.4573)	info on Rv1879/-
Rv1225c/-	(cc=0.4465)	info on Rv1225c/-
Rv2887/-	(cc=0.4386)	info on Rv2887/-
Rv0328/-	(cc=0.4369)	info on Rv0328/-
Rv1665/pks11	(cc=0.4259)	info on Rv1665/pks11
Rv2218/lipA	(cc=0.418)	info on Rv2218/lipA
Rv1831/-	(cc=0.4171)	info on Rv1831/-
Rv1748/-	(cc=0.4107)	info on Rv1748/-
Rv1398c/vapB10	(cc=0.4008)	info on Rv1398c/vapB10

Correlation of Rv3698/- with Rv1748/-

Normalized LFCs for Rv3698/-:
(description and provenance of datasets)

	Rv3698/-	Rv1748/-
Fe_supp_jason_reseq	0.286	0.111
low_pH_jason_reseq	-0.489	-0.858
NO_jason_reseq	-1.173	0.184
B6_jason_reseq	-0.324	-0.016
MHCII_jason_reseq	1.101	0.442
Isoniazid02	-0.16	0.291
Rifampicin4	-0.298	0.014
Ethambutol3	1.987	2.101
Meropenem3	1.198	0.552
Vancomycin16	0.111	-0.085
Rv2680_day32	0.204	-0.393
H37Rv_KO_MarP	0.871	0.947
hypoxia_3wks	0.383	0.279
hypoxia_6wks	0.0	-0.37
glycerol	0.312	0.652
cholesterol	0.146	0.316
AJ	-0.183	0.592
Bibs02	-0.085	0.669
Bibs02c	0.323	-0.1
BL6	0.303	0.874
BL6a	0.55	0.633
BXD01	0.924	0.744
BXD010	0.496	0.875
BXD011	0.508	0.557
BXD03	0.989	0.565
BXD04	1.336	1.697
BXD05	0.766	0.33
BXD06	0.37	0.573
BXD07	0.384	0.952
BXD08	1.061	1.296
BXD09	0.272	0.669
CAST	-0.502	-0.12
CCcont	1.024	0.687
DS01	0.334	0.371
DS02	0.096	-0.134
DS04	0.299	0.703
DS0c	1.365	0.581
GP01	0.297	0.384
GP02	0.764	0.45
GP0c	0.491	0.467
NOD	-0.329	0.112
NZO	-0.672	0.066
PWK	0.252	0.098
H37Rv_KO_CtpC	-0.325	0.331
H37Rv_KO_CtpD	0.366	-0.505
H37Rv_KO_Rv1272	0.375	0.336
H37Rv_KO_SugABC	0.374	1.04
H37Rv_KO_MbtN	0.132	0.788
Trans05	0.408	1.171
macrophage_unactivated	2.149	0.71
IL1	-0.059	-0.231
Rapamycin	0.976	0.335
Tcell	1.189	0.068
GMCSF	0.053	0.869
IFNab	1.103	0.063
IFNg	0.722	-0.257
IFNg_GMCSF1	0.528	0.053
Rv1432_day32	0.021	-0.379
Rv1565c_day32	-0.283	0.851
secA2_input	-0.163	0.197
delta_Rv3594	0.967	0.545
delta_Rv3717	-0.191	0.398
delta_Rv3811	-0.138	0.281
delta_Rv0954	1.083	0.488
PonA1	-0.043	0.495
EccD1_KO	0.405	-0.059
EspI_KO	0.516	0.051
PE35_KO	0.461	-0.064
PPE68_KO	0.653	0.07
glycerol2	0.042	-0.671
lignocerate	0.239	-0.192
oleate	0.333	0.153
phosphatidylcholine	0.434	-0.062
acetate	0.326	-0.953
glucAc	0.381	-0.916
Rv0950ko	0.262	1.073
Rv1096ko	-0.139	0.015
Rv3684ko	-0.717	0.619
delta_otsA_trehalose	-0.439	-0.348