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 Rv3301c/phoY1:

update plot	correlation	link to info on gene
Rv2623/TB31.7	(cc=0.5231)	info on Rv2623/TB31.7
Rv2813/-	(cc=0.51)	info on Rv2813/-
Rv2544/lppB	(cc=0.5047)	info on Rv2544/lppB
Rv2960c/-	(cc=0.5033)	info on Rv2960c/-
Rv1987/-	(cc=0.4721)	info on Rv1987/-
Rv3045/adhC	(cc=0.4665)	info on Rv3045/adhC
Rv3010c/pfkA	(cc=0.4648)	info on Rv3010c/pfkA
Rv3133c/devR	(cc=0.4559)	info on Rv3133c/devR
Rv0945/-	(cc=0.454)	info on Rv0945/-
Rv2276/cyp121	(cc=0.4518)	info on Rv2276/cyp121

Correlation of Rv3301c/phoY1 with Rv2544/lppB

Normalized LFCs for Rv3301c/phoY1:
(description and provenance of datasets)

	Rv3301c/phoY1	Rv2544/lppB
Fe_supp_jason_reseq	0.633	1.127
low_pH_jason_reseq	-0.515	-1.017
NO_jason_reseq	0.189	0.173
B6_jason_reseq	-0.846	0.024
MHCII_jason_reseq	1.171	-1.788
Isoniazid02	-0.781	0.0
Rifampicin4	-1.362	-0.883
Ethambutol3	-0.741	-0.353
Meropenem3	-0.521	-0.391
Vancomycin16	-0.783	0.799
Rv2680_day32	-0.799	0.305
H37Rv_KO_MarP	0.04	-0.246
hypoxia_3wks	-3.369	-0.813
hypoxia_6wks	-2.648	-0.115
glycerol	-0.167	0.06
cholesterol	-1.3	-0.184
AJ	-0.425	-0.071
Bibs02	-0.539	0.437
Bibs02c	0.144	1.105
BL6	1.166	1.373
BL6a	0.263	1.738
BXD01	0.677	1.583
BXD010	0.399	1.615
BXD011	0.494	1.618
BXD03	0.301	1.844
BXD04	-0.033	1.957
BXD05	-0.086	1.846
BXD06	0.297	1.135
BXD07	0.562	1.284
BXD08	0.602	1.041
BXD09	0.429	1.435
CAST	0.12	-0.908
CCcont	0.633	1.744
DS01	0.041	0.137
DS02	-1.186	-0.276
DS04	0.417	0.554
DS0c	0.149	-0.275
GP01	-1.522	-0.745
GP02	-0.898	-0.444
GP0c	0.27	-0.83
NOD	0.516	-0.361
NZO	-0.224	-0.253
PWK	-0.487	1.172
H37Rv_KO_CtpC	0.698	2.292
H37Rv_KO_CtpD	-0.71	1.467
H37Rv_KO_Rv1272	0.476	1.852
H37Rv_KO_SugABC	1.505	1.493
H37Rv_KO_MbtN	0.399	2.949
Trans05	-0.325	1.969
macrophage_unactivated	-0.436	0.249
IL1	-0.457	0.178
Rapamycin	0.74	0.061
Tcell	0.746	0.56
GMCSF	0.0	0.309
IFNab	0.692	0.296
IFNg	0.612	0.828
IFNg_GMCSF1	0.984	1.901
Rv1432_day32	0.073	0.035
Rv1565c_day32	1.264	1.311
secA2_input	-0.454	-0.606
delta_Rv3594	0.26	1.201
delta_Rv3717	-0.216	0.055
delta_Rv3811	0.229	0.86
delta_Rv0954	1.689	0.727
PonA1	-0.223	0.075
EccD1_KO	1.246	0.059
EspI_KO	0.633	0.485
PE35_KO	0.648	0.855
PPE68_KO	0.486	0.841
glycerol2	0.736	2.159
lignocerate	1.136	2.678
oleate	0.469	-1.239
phosphatidylcholine	0.958	2.189
acetate	1.589	2.909
glucAc	1.487	2.554
Rv0950ko	-0.543	0.121
Rv1096ko	0.154	-0.712
Rv3684ko	-1.431	-0.517
delta_otsA_trehalose	-1.061	-0.318