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 Rv3900c/-:

update plot	correlation	link to info on gene
Rv3537/kstD	(cc=0.5508)	info on Rv3537/kstD
Rv1729c/-	(cc=0.4953)	info on Rv1729c/-
Rv3762c/-	(cc=0.4834)	info on Rv3762c/-
Rv0250c/-	(cc=0.4772)	info on Rv0250c/-
Rv1059/-	(cc=0.4726)	info on Rv1059/-
Rv2929/-	(cc=0.4714)	info on Rv2929/-
Rv3429/PPE59	(cc=0.4696)	info on Rv3429/PPE59
Rv3146/nuoB	(cc=0.4689)	info on Rv3146/nuoB
Rv1870c/-	(cc=0.461)	info on Rv1870c/-
Rv1207/folP2	(cc=0.4518)	info on Rv1207/folP2

Correlation of Rv3900c/- with Rv3429/PPE59

Normalized LFCs for Rv3900c/-:
(description and provenance of datasets)

	Rv3900c/-	Rv3429/PPE59
Fe_supp_jason_reseq	-0.406	0.628
low_pH_jason_reseq	0.632	0.202
NO_jason_reseq	-0.352	-0.029
B6_jason_reseq	-0.285	-1.06
MHCII_jason_reseq	-0.876	0.265
Isoniazid02	-0.226	-0.125
Rifampicin4	0.544	-0.566
Ethambutol3	0.946	1.225
Meropenem3	1.216	1.438
Vancomycin16	0.228	0.215
Rv2680_day32	-0.763	-0.23
H37Rv_KO_MarP	0.679	0.346
hypoxia_3wks	0.49	0.0
hypoxia_6wks	-0.077	0.069
glycerol	-0.24	-1.568
cholesterol	-0.243	-0.909
AJ	-0.439	0.382
Bibs02	-0.631	-0.276
Bibs02c	-0.878	0.412
BL6	0.272	1.223
BL6a	-0.105	1.017
BXD01	0.446	1.398
BXD010	0.597	1.497
BXD011	0.116	1.714
BXD03	0.236	0.988
BXD04	0.63	0.307
BXD05	0.225	1.232
BXD06	0.749	1.426
BXD07	0.413	1.178
BXD08	0.497	1.307
BXD09	0.7	1.463
CAST	0.117	0.379
CCcont	0.838	0.942
DS01	-0.021	0.77
DS02	-0.884	0.668
DS04	0.748	1.026
DS0c	-0.671	0.728
GP01	0.801	1.468
GP02	-0.257	0.874
GP0c	0.689	1.149
NOD	0.094	0.443
NZO	-0.712	0.516
PWK	-0.196	0.602
H37Rv_KO_CtpC	-0.042	1.547
H37Rv_KO_CtpD	1.454	1.898
H37Rv_KO_Rv1272	0.336	0.86
H37Rv_KO_SugABC	0.8	1.451
H37Rv_KO_MbtN	0.202	0.74
Trans05	-0.034	1.42
macrophage_unactivated	0.451	0.417
IL1	0.311	0.658
Rapamycin	0.368	-0.203
Tcell	-0.137	1.121
GMCSF	0.214	-0.412
IFNab	0.339	-0.411
IFNg	0.0	0.216
IFNg_GMCSF1	-0.647	-0.459
Rv1432_day32	-0.469	0.09
Rv1565c_day32	-0.058	-1.088
secA2_input	0.177	-0.399
delta_Rv3594	-0.054	-0.722
delta_Rv3717	-0.736	-0.812
delta_Rv3811	0.241	-0.366
delta_Rv0954	-0.261	-0.397
PonA1	-0.07	-0.518
EccD1_KO	-0.582	0.224
EspI_KO	-0.884	0.408
PE35_KO	-0.137	0.548
PPE68_KO	-0.086	0.189
glycerol2	0.294	0.426
lignocerate	0.203	0.591
oleate	0.089	0.417
phosphatidylcholine	-0.057	0.916
acetate	-0.361	0.472
glucAc	-0.205	0.483
Rv0950ko	0.109	0.422
Rv1096ko	-0.802	-0.582
Rv3684ko	-0.098	-0.54
delta_otsA_trehalose	-0.73	0.083