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 Rv1579c/-

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

	Rv1672c/-	Rv1579c/-
Fe_supp_jason_reseq	0.388	0.379
low_pH_jason_reseq	-0.549	-0.023
NO_jason_reseq	0.163	0.475
B6_jason_reseq	-0.295	-0.016
MHCII_jason_reseq	-0.09	0.814
Isoniazid02	1.635	3.529
Rifampicin4	-0.089	0.517
Ethambutol3	2.692	3.803
Meropenem3	0.412	0.34
Vancomycin16	0.329	0.753
Rv2680_day32	-0.656	-0.554
H37Rv_KO_MarP	-0.425	-0.825
hypoxia_3wks	0.861	0.048
hypoxia_6wks	1.746	-0.735
glycerol	0.392	0.206
cholesterol	0.017	0.614
AJ	0.358	-1.874
Bibs02	0.225	-2.099
Bibs02c	-0.209	0.136
BL6	0.231	-0.841
BL6a	0.092	0.273
BXD01	0.146	0.994
BXD010	0.502	0.423
BXD011	0.0	-0.619
BXD03	0.461	0.105
BXD04	0.24	1.109
BXD05	-0.016	-0.466
BXD06	-0.032	1.219
BXD07	0.722	1.17
BXD08	0.205	-0.275
BXD09	0.628	0.911
CAST	-0.055	-0.295
CCcont	0.017	0.736
DS01	0.137	0.958
DS02	0.904	0.142
DS04	0.09	-0.672
DS0c	0.627	1.497
GP01	0.068	-1.849
GP02	0.47	-1.275
GP0c	-0.218	-2.791
NOD	-0.345	-1.751
NZO	0.224	0.104
PWK	0.242	-0.539
H37Rv_KO_CtpC	0.267	-1.051
H37Rv_KO_CtpD	0.443	-0.143
H37Rv_KO_Rv1272	-0.178	-1.139
H37Rv_KO_SugABC	-0.208	1.045
H37Rv_KO_MbtN	0.37	-1.104
Trans05	0.365	-0.228
macrophage_unactivated	-0.107	0.391
IL1	0.033	0.611
Rapamycin	0.267	-1.924
Tcell	0.991	-0.893
GMCSF	0.37	-0.074
IFNab	-0.139	-1.001
IFNg	0.535	0.802
IFNg_GMCSF1	0.207	0.0
Rv1432_day32	2.048	0.18
Rv1565c_day32	0.6	0.166
secA2_input	-0.257	-0.131
delta_Rv3594	0.439	-0.014
delta_Rv3717	0.072	-1.402
delta_Rv3811	0.596	-0.503
delta_Rv0954	0.127	-0.084
PonA1	-0.57	-1.558
EccD1_KO	-0.385	-1.168
EspI_KO	-0.55	-1.743
PE35_KO	0.694	-0.709
PPE68_KO	0.544	-1.014
glycerol2	-0.165	0.039
lignocerate	-0.166	-0.587
oleate	0.176	0.318
phosphatidylcholine	0.067	0.09
acetate	-0.286	0.612
glucAc	-0.086	-0.653
Rv0950ko	0.039	-1.233
Rv1096ko	0.157	-0.657
Rv3684ko	0.128	-1.464
delta_otsA_trehalose	-0.96	-0.323