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 Rv1564c/treX:

update plot	correlation	link to info on gene
Rv3363c/-	(cc=0.5751)	info on Rv3363c/-
Rv3168/-	(cc=0.5383)	info on Rv3168/-
Rv3218/-	(cc=0.479)	info on Rv3218/-
Rv0045c/-	(cc=0.4724)	info on Rv0045c/-
Rv1513/-	(cc=0.4578)	info on Rv1513/-
Rv2655c/-	(cc=0.4573)	info on Rv2655c/-
Rv0551c/fadD8	(cc=0.457)	info on Rv0551c/fadD8
Rv3320c/vapC44	(cc=0.4508)	info on Rv3320c/vapC44
Rv0592/mce2D	(cc=0.4396)	info on Rv0592/mce2D
Rv0112/gca	(cc=0.4356)	info on Rv0112/gca

Correlation of Rv1564c/treX with Rv0592/mce2D

Normalized LFCs for Rv1564c/treX:
(description and provenance of datasets)

	Rv1564c/treX	Rv0592/mce2D
Fe_supp_jason_reseq	0.115	0.622
low_pH_jason_reseq	0.877	-0.049
NO_jason_reseq	0.617	0.144
B6_jason_reseq	1.042	0.552
MHCII_jason_reseq	0.449	0.342
Isoniazid02	0.048	0.06
Rifampicin4	0.845	-0.68
Ethambutol3	0.395	-0.43
Meropenem3	1.053	0.497
Vancomycin16	0.417	0.109
Rv2680_day32	0.667	-0.357
H37Rv_KO_MarP	0.742	-0.135
hypoxia_3wks	1.902	-0.124
hypoxia_6wks	0.647	0.217
glycerol	-0.344	-0.298
cholesterol	-0.247	-0.358
AJ	0.166	0.299
Bibs02	0.409	0.323
Bibs02c	-0.039	0.488
BL6	0.985	0.835
BL6a	0.29	0.08
BXD01	0.412	0.599
BXD010	0.482	0.212
BXD011	0.463	-0.054
BXD03	0.544	0.56
BXD04	0.357	0.261
BXD05	0.607	0.072
BXD06	0.658	-0.134
BXD07	0.931	0.127
BXD08	0.226	0.171
BXD09	0.356	-0.142
CAST	0.697	0.889
CCcont	-0.028	-0.173
DS01	-0.852	0.577
DS02	-0.517	0.227
DS04	-0.885	0.943
DS0c	-0.841	0.732
GP01	0.969	0.521
GP02	0.217	0.055
GP0c	0.464	-0.255
NOD	-0.241	0.473
NZO	0.851	0.257
PWK	1.611	0.347
H37Rv_KO_CtpC	-0.586	0.517
H37Rv_KO_CtpD	-0.346	0.525
H37Rv_KO_Rv1272	-0.319	-0.122
H37Rv_KO_SugABC	0.293	-1.55
H37Rv_KO_MbtN	1.052	-0.273
Trans05	0.222	-0.716
macrophage_unactivated	0.0	0.48
IL1	0.258	-0.122
Rapamycin	-0.08	0.239
Tcell	-0.085	0.375
GMCSF	0.0	0.401
IFNab	-0.039	-0.06
IFNg	0.102	0.259
IFNg_GMCSF1	0.352	0.126
Rv1432_day32	0.997	1.352
Rv1565c_day32	0.103	0.377
secA2_input	-0.753	-0.081
delta_Rv3594	-0.621	0.121
delta_Rv3717	0.17	-0.247
delta_Rv3811	-0.631	-0.223
delta_Rv0954	-0.255	-0.654
PonA1	-0.557	0.069
EccD1_KO	-1.503	-0.664
EspI_KO	-1.101	-0.359
PE35_KO	-0.379	-0.89
PPE68_KO	-0.806	-0.586
glycerol2	-0.926	-0.021
lignocerate	-0.788	-0.253
oleate	-0.917	-0.223
phosphatidylcholine	-0.711	-0.085
acetate	-0.404	-0.374
glucAc	-0.206	-0.529
Rv0950ko	-0.112	0.89
Rv1096ko	-0.29	0.983
Rv3684ko	-0.445	-0.193
delta_otsA_trehalose	3.876	3.282