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 Rv1672c/-:

update plot	correlation	link to info on gene
Rv0454/-	(cc=0.4989)	info on Rv0454/-
Rv1215c/-	(cc=0.4562)	info on Rv1215c/-
Rv2333c/stp	(cc=0.4353)	info on Rv2333c/stp
Rv1579c/-	(cc=0.4329)	info on Rv1579c/-
Rv0532/PE_PGRS6	(cc=0.4313)	info on Rv0532/PE_PGRS6
Rv3174/-	(cc=0.4286)	info on Rv3174/-
Rv1105/-	(cc=0.4182)	info on Rv1105/-
Rv1290c/-	(cc=0.418)	info on Rv1290c/-
Rv0078A/-	(cc=0.4078)	info on Rv0078A/-
Rv1482c/-	(cc=0.4058)	info on Rv1482c/-

Correlation of Rv1672c/- with Rv1215c/-

Normalized LFCs for Rv1672c/-:
(description and provenance of datasets)

	Rv1672c/-	Rv1215c/-
Fe_supp_jason_reseq	0.388	-0.272
low_pH_jason_reseq	-0.549	0.11
NO_jason_reseq	0.163	0.339
B6_jason_reseq	-0.295	-0.613
MHCII_jason_reseq	-0.09	-1.388
Isoniazid02	1.635	0.755
Rifampicin4	-0.089	0.441
Ethambutol3	2.692	2.03
Meropenem3	0.412	0.919
Vancomycin16	0.329	0.276
Rv2680_day32	-0.656	0.171
H37Rv_KO_MarP	-0.425	0.334
hypoxia_3wks	0.861	0.622
hypoxia_6wks	1.746	0.0
glycerol	0.392	-0.127
cholesterol	0.017	0.069
AJ	0.358	0.536
Bibs02	0.225	-0.399
Bibs02c	-0.209	-0.488
BL6	0.231	0.418
BL6a	0.092	0.141
BXD01	0.146	0.339
BXD010	0.502	0.527
BXD011	0.0	1.165
BXD03	0.461	0.172
BXD04	0.24	0.158
BXD05	-0.016	0.27
BXD06	-0.032	0.515
BXD07	0.722	0.25
BXD08	0.205	0.743
BXD09	0.628	0.53
CAST	-0.055	0.509
CCcont	0.017	0.054
DS01	0.137	0.058
DS02	0.904	0.323
DS04	0.09	0.093
DS0c	0.627	0.079
GP01	0.068	0.529
GP02	0.47	1.583
GP0c	-0.218	0.077
NOD	-0.345	-0.172
NZO	0.224	0.98
PWK	0.242	0.117
H37Rv_KO_CtpC	0.267	0.721
H37Rv_KO_CtpD	0.443	0.5
H37Rv_KO_Rv1272	-0.178	0.837
H37Rv_KO_SugABC	-0.208	-0.024
H37Rv_KO_MbtN	0.37	0.297
Trans05	0.365	0.601
macrophage_unactivated	-0.107	-0.186
IL1	0.033	-0.264
Rapamycin	0.267	-0.181
Tcell	0.991	0.14
GMCSF	0.37	-0.037
IFNab	-0.139	0.088
IFNg	0.535	-0.238
IFNg_GMCSF1	0.207	-0.632
Rv1432_day32	2.048	1.285
Rv1565c_day32	0.6	0.092
secA2_input	-0.257	-0.604
delta_Rv3594	0.439	-0.194
delta_Rv3717	0.072	-0.932
delta_Rv3811	0.596	-0.598
delta_Rv0954	0.127	-0.872
PonA1	-0.57	-0.016
EccD1_KO	-0.385	0.457
EspI_KO	-0.55	0.311
PE35_KO	0.694	0.405
PPE68_KO	0.544	0.253
glycerol2	-0.165	-0.031
lignocerate	-0.166	-0.054
oleate	0.176	0.593
phosphatidylcholine	0.067	0.539
acetate	-0.286	-0.409
glucAc	-0.086	-0.644
Rv0950ko	0.039	-0.347
Rv1096ko	0.157	0.042
Rv3684ko	0.128	-0.331
delta_otsA_trehalose	-0.96	-0.673