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 Rv0040c/mtc28:
Show top 50 genes. Show bottom 10 genes with LOWEST correlation.

Most correlated genes.

update plot	correlation	link to info on gene
Rv1006/-	(cc=0.5509)	info on Rv1006/-
Rv0999/-	(cc=0.5472)	info on Rv0999/-
Rv3005c/-	(cc=0.5171)	info on Rv3005c/-
Rv2363/amiA2	(cc=0.5153)	info on Rv2363/amiA2
Rv2170/-	(cc=0.5063)	info on Rv2170/-
Rv2869c/rip	(cc=0.5005)	info on Rv2869c/rip
Rv2224c/caeA	(cc=0.4975)	info on Rv2224c/caeA
Rv3207c/-	(cc=0.4961)	info on Rv3207c/-
Rv1566c/-	(cc=0.4925)	info on Rv1566c/-
Rv0950c/-	(cc=0.4861)	info on Rv0950c/-

Correlation of Rv0040c/mtc28 with Rv1006/-

Normalized LFCs for Rv0040c/mtc28:
(description and provenance of datasets)

Comparison of LFCs between selected condtions.

condition	Rv0040c/mtc28	Rv1006/-
Fe_supp_jason_reseq	2.742	2.892
low_pH_jason_reseq	-1.116	0.596
NO_jason_reseq	-1.643	-0.845
B6_jason_reseq	-1.298	-0.357
MHCII_jason_reseq	0.125	1.742
Isoniazid02	-1.157	0.071
Rifampicin4	-2.434	-5.058
Ethambutol3	-0.776	0.766
Meropenem3	-1.511	-1.508
Vancomycin16	-1.897	-3.404
Rv2680_day32	-0.178	-0.793
H37Rv_KO_MarP	-1.239	-2.348
hypoxia_3wks	-0.989	-0.574
hypoxia_6wks	-1.105	-1.84
glycerol	-1.021	1.005
cholesterol	0.621	0.957
AJ	-1.067	-0.551
Bibs02	-0.648	0.828
Bibs02c	0.358	1.343
BL6	-1.078	0.462
BL6a	0.501	0.943
BXD01	-0.488	0.497
BXD010	-0.379	-0.169
BXD011	-0.736	-0.093
BXD03	-0.506	0.115
BXD04	1.229	0.202
BXD05	-0.745	-0.233
BXD06	-1.026	-0.508
BXD07	-0.214	-0.101
BXD08	-1.191	0.135
BXD09	-0.959	0.119
CAST	-0.681	-1.473
CCcont	0.309	1.936
DS01	-0.034	0.491
DS02	-0.063	0.775
DS04	1.46	0.197
DS0c	-0.812	1.328
GP01	1.266	-0.054
GP02	0.058	-0.712
GP0c	0.773	-0.598
NOD	-0.421	-1.095
NZO	-0.831	-0.345
PWK	-2.367	-1.191
H37Rv_KO_CtpC	1.257	1.233
H37Rv_KO_CtpD	1.944	1.748
H37Rv_KO_Rv1272	1.072	0.273
H37Rv_KO_SugABC	-0.992	0.525
H37Rv_KO_MbtN	0.412	0.455
Trans05	0.713	-0.254
macrophage_unactivated	-0.164	1.793
IL1	-0.537	-0.154
Rapamycin	1.182	1.114
Tcell	-0.525	0.166
GMCSF	-0.28	0.626
IFNab	0.665	0.444
IFNg	-0.233	0.0
IFNg_GMCSF1	0.053	0.314
Rv1432_day32	-1.555	0.228
Rv1565c_day32	-2.071	0.734
secA2_input	0.138	-0.207
delta_Rv3594	-0.463	1.345
delta_Rv3717	-0.118	0.19
delta_Rv3811	-0.265	0.953
delta_Rv0954	-0.264	1.578
PonA1	0.755	0.646
EccD1_KO	-0.802	-0.908
EspI_KO	0.262	-0.445
PE35_KO	-0.175	-0.738
PPE68_KO	-0.192	0.182
glycerol2	-0.509	-0.553
lignocerate	0.032	0.308
oleate	-1.157	0.0
phosphatidylcholine	-0.573	-0.021
acetate	-0.419	0.025
glucAc	-0.26	-0.269
Rv0950ko	-1.185	-2.439
Rv1096ko	-0.118	-1.384
Rv3684ko	-0.062	-0.229
delta_otsA_trehalose	-0.486	-0.348