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 Rv2960c/-

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

	Rv3301c/phoY1	Rv2960c/-
Fe_supp_jason_reseq	0.633	1.135
low_pH_jason_reseq	-0.515	-1.29
NO_jason_reseq	0.189	-0.756
B6_jason_reseq	-0.846	1.024
MHCII_jason_reseq	1.171	0.959
Isoniazid02	-0.781	-0.287
Rifampicin4	-1.362	0.084
Ethambutol3	-0.741	1.799
Meropenem3	-0.521	-0.775
Vancomycin16	-0.783	-0.276
Rv2680_day32	-0.799	1.608
H37Rv_KO_MarP	0.04	-1.116
hypoxia_3wks	-3.369	-0.048
hypoxia_6wks	-2.648	-1.029
glycerol	-0.167	-0.835
cholesterol	-1.3	-0.459
AJ	-0.425	-0.55
Bibs02	-0.539	-1.057
Bibs02c	0.144	0.929
BL6	1.166	0.902
BL6a	0.263	0.656
BXD01	0.677	0.378
BXD010	0.399	-0.228
BXD011	0.494	0.649
BXD03	0.301	0.612
BXD04	-0.033	0.777
BXD05	-0.086	0.767
BXD06	0.297	-0.144
BXD07	0.562	0.97
BXD08	0.602	0.666
BXD09	0.429	0.493
CAST	0.12	-0.145
CCcont	0.633	1.087
DS01	0.041	0.033
DS02	-1.186	-0.709
DS04	0.417	0.708
DS0c	0.149	0.225
GP01	-1.522	0.039
GP02	-0.898	0.907
GP0c	0.27	-0.082
NOD	0.516	0.799
NZO	-0.224	-1.351
PWK	-0.487	-0.182
H37Rv_KO_CtpC	0.698	0.692
H37Rv_KO_CtpD	-0.71	0.59
H37Rv_KO_Rv1272	0.476	1.133
H37Rv_KO_SugABC	1.505	1.602
H37Rv_KO_MbtN	0.399	-0.726
Trans05	-0.325	-0.181
macrophage_unactivated	-0.436	0.521
IL1	-0.457	0.119
Rapamycin	0.74	-0.574
Tcell	0.746	0.215
GMCSF	0.0	0.325
IFNab	0.692	-0.166
IFNg	0.612	0.409
IFNg_GMCSF1	0.984	1.002
Rv1432_day32	0.073	0.3
Rv1565c_day32	1.264	0.444
secA2_input	-0.454	-1.262
delta_Rv3594	0.26	0.541
delta_Rv3717	-0.216	0.573
delta_Rv3811	0.229	0.677
delta_Rv0954	1.689	1.623
PonA1	-0.223	0.502
EccD1_KO	1.246	1.48
EspI_KO	0.633	0.582
PE35_KO	0.648	0.755
PPE68_KO	0.486	0.998
glycerol2	0.736	1.892
lignocerate	1.136	2.72
oleate	0.469	-0.829
phosphatidylcholine	0.958	1.982
acetate	1.589	2.555
glucAc	1.487	2.555
Rv0950ko	-0.543	-1.025
Rv1096ko	0.154	0.332
Rv3684ko	-1.431	-0.108
delta_otsA_trehalose	-1.061	0.347