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 Rv3023c/-:

update plot	correlation	link to info on gene
Rv1047/-	(cc=0.9569)	info on Rv1047/-
Rv2666/-	(cc=0.8829)	info on Rv2666/-
Rv3115/-	(cc=0.8696)	info on Rv3115/-
Rv2512c/-	(cc=0.7659)	info on Rv2512c/-
Rv1199c/-	(cc=0.7634)	info on Rv1199c/-
Rv3187/-	(cc=0.689)	info on Rv3187/-
Rv2279/-	(cc=0.6867)	info on Rv2279/-
Rv1369c/-	(cc=0.6681)	info on Rv1369c/-
Rv1756c/-	(cc=0.6668)	info on Rv1756c/-
Rv2355/-	(cc=0.6589)	info on Rv2355/-

Correlation of Rv3023c/- with Rv2512c/-

Normalized LFCs for Rv3023c/-:
(description and provenance of datasets)

	Rv3023c/-	Rv2512c/-
Fe_supp_jason_reseq	-0.908	-0.661
low_pH_jason_reseq	-0.186	-0.325
NO_jason_reseq	-0.155	-0.478
B6_jason_reseq	-0.704	-0.327
MHCII_jason_reseq	-0.428	-0.315
Isoniazid02	-1.075	-0.905
Rifampicin4	0.257	0.536
Ethambutol3	-0.631	-0.45
Meropenem3	-0.294	-0.153
Vancomycin16	-0.82	-0.533
Rv2680_day32	0.098	0.201
H37Rv_KO_MarP	-0.222	-0.032
hypoxia_3wks	-0.215	0.104
hypoxia_6wks	-0.785	-0.349
glycerol	0.234	0.37
cholesterol	-0.17	-0.189
AJ	0.931	0.913
Bibs02	1.028	1.052
Bibs02c	1.42	1.346
BL6	0.027	-0.057
BL6a	0.809	0.839
BXD01	0.532	0.42
BXD010	0.523	0.392
BXD011	0.257	0.221
BXD03	0.679	0.285
BXD04	0.743	0.551
BXD05	0.952	0.906
BXD06	0.575	0.293
BXD07	0.823	0.627
BXD08	0.328	0.1
BXD09	0.453	0.383
CAST	0.762	0.781
CCcont	0.065	0.081
DS01	0.366	0.838
DS02	0.985	1.108
DS04	0.528	0.906
DS0c	0.837	0.998
GP01	0.433	0.235
GP02	0.489	0.262
GP0c	0.32	0.138
NOD	0.688	0.724
NZO	0.578	0.561
PWK	0.466	0.568
H37Rv_KO_CtpC	1.194	0.965
H37Rv_KO_CtpD	0.662	0.345
H37Rv_KO_Rv1272	0.747	0.669
H37Rv_KO_SugABC	1.049	0.875
H37Rv_KO_MbtN	0.437	0.129
Trans05	1.11	0.925
macrophage_unactivated	0.268	-0.076
IL1	0.925	-0.377
Rapamycin	0.638	-0.727
Tcell	-1.039	-1.639
GMCSF	0.85	-0.37
IFNab	0.29	-0.846
IFNg	0.032	-0.633
IFNg_GMCSF1	0.688	-0.698
Rv1432_day32	-0.402	-0.452
Rv1565c_day32	0.253	-0.455
secA2_input	-0.139	-0.346
delta_Rv3594	0.104	0.0
delta_Rv3717	-0.37	-0.081
delta_Rv3811	0.0	0.162
delta_Rv0954	-0.056	-0.118
PonA1	-0.716	-0.851
EccD1_KO	-0.408	0.441
EspI_KO	0.083	0.525
PE35_KO	1.0	1.202
PPE68_KO	0.278	1.075
glycerol2	-1.386	-0.929
lignocerate	-1.078	-0.435
oleate	-1.171	-1.026
phosphatidylcholine	-1.104	-0.641
acetate	0.685	1.069
glucAc	-0.081	0.264
Rv0950ko	0.0	-0.033
Rv1096ko	-0.489	-0.944
Rv3684ko	-0.301	-1.215
delta_otsA_trehalose	-0.437	-1.117