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 Rv2277c/-:

update plot	correlation	link to info on gene
Rv1917c/PPE34	(cc=0.4558)	info on Rv1917c/PPE34
Rv1501/-	(cc=0.4073)	info on Rv1501/-
Rv3667/acs	(cc=0.4038)	info on Rv3667/acs
Rv1550/fadD11	(cc=0.4036)	info on Rv1550/fadD11
Rv1892/-	(cc=0.3983)	info on Rv1892/-
Rv2544/lppB	(cc=0.3978)	info on Rv2544/lppB
Rv3858c/gltD	(cc=0.3973)	info on Rv3858c/gltD
Rv0059/-	(cc=0.3947)	info on Rv0059/-
Rv3528c/-	(cc=0.3861)	info on Rv3528c/-
Rv2256c/-	(cc=0.386)	info on Rv2256c/-

Correlation of Rv2277c/- with Rv2544/lppB

Normalized LFCs for Rv2277c/-:
(description and provenance of datasets)

	Rv2277c/-	Rv2544/lppB
Fe_supp_jason_reseq	0.137	1.127
low_pH_jason_reseq	-0.905	-1.017
NO_jason_reseq	-0.079	0.173
B6_jason_reseq	0.757	0.024
MHCII_jason_reseq	0.47	-1.788
Isoniazid02	0.426	0.0
Rifampicin4	-0.412	-0.883
Ethambutol3	-0.259	-0.353
Meropenem3	-0.044	-0.391
Vancomycin16	0.321	0.799
Rv2680_day32	0.776	0.305
H37Rv_KO_MarP	0.574	-0.246
hypoxia_3wks	-0.331	-0.813
hypoxia_6wks	-0.265	-0.115
glycerol	-0.417	0.06
cholesterol	-0.192	-0.184
AJ	-0.15	-0.071
Bibs02	-0.848	0.437
Bibs02c	0.064	1.105
BL6	-0.611	1.373
BL6a	0.09	1.738
BXD01	0.816	1.583
BXD010	0.334	1.615
BXD011	-0.125	1.618
BXD03	0.268	1.844
BXD04	0.056	1.957
BXD05	-0.064	1.846
BXD06	0.365	1.135
BXD07	0.717	1.284
BXD08	0.701	1.041
BXD09	0.349	1.435
CAST	0.07	-0.908
CCcont	0.155	1.744
DS01	-0.152	0.137
DS02	-0.665	-0.276
DS04	-0.899	0.554
DS0c	-0.035	-0.275
GP01	-0.016	-0.745
GP02	-0.448	-0.444
GP0c	-1.395	-0.83
NOD	-0.734	-0.361
NZO	-0.449	-0.253
PWK	0.759	1.172
H37Rv_KO_CtpC	-0.603	2.292
H37Rv_KO_CtpD	0.582	1.467
H37Rv_KO_Rv1272	-0.291	1.852
H37Rv_KO_SugABC	1.029	1.493
H37Rv_KO_MbtN	0.847	2.949
Trans05	0.403	1.969
macrophage_unactivated	0.114	0.249
IL1	-0.516	0.178
Rapamycin	-0.23	0.061
Tcell	0.508	0.56
GMCSF	-0.048	0.309
IFNab	0.109	0.296
IFNg	0.144	0.828
IFNg_GMCSF1	-0.613	1.901
Rv1432_day32	-0.562	0.035
Rv1565c_day32	0.663	1.311
secA2_input	-0.834	-0.606
delta_Rv3594	0.139	1.201
delta_Rv3717	-0.896	0.055
delta_Rv3811	-0.057	0.86
delta_Rv0954	-0.731	0.727
PonA1	0.063	0.075
EccD1_KO	-1.424	0.059
EspI_KO	-0.719	0.485
PE35_KO	-0.379	0.855
PPE68_KO	-0.806	0.841
glycerol2	0.119	2.159
lignocerate	-0.149	2.678
oleate	0.411	-1.239
phosphatidylcholine	0.438	2.189
acetate	0.339	2.909
glucAc	0.57	2.554
Rv0950ko	-0.859	0.121
Rv1096ko	-1.601	-0.712
Rv3684ko	-0.445	-0.517
delta_otsA_trehalose	-1.577	-0.318