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 Rv3413c/-:
Show top 50 genes. Show bottom 10 genes with LOWEST correlation.

Most correlated genes.

update plot	correlation	link to info on gene
Rv1846c/blaI	(cc=0.6366)	info on Rv1846c/blaI
Rv3005c/-	(cc=0.5405)	info on Rv3005c/-
Rv3717/-	(cc=0.5143)	info on Rv3717/-
Rv0994/moeA1	(cc=0.5005)	info on Rv0994/moeA1
Rv0406c/-	(cc=0.4952)	info on Rv0406c/-
Rv2564/glnQ	(cc=0.4907)	info on Rv2564/glnQ
Rv3661/-	(cc=0.4772)	info on Rv3661/-
Rv2125/-	(cc=0.4703)	info on Rv2125/-
Rv0561c/-	(cc=0.4689)	info on Rv0561c/-
Rv2563/-	(cc=0.4586)	info on Rv2563/-

Correlation of Rv3413c/- with Rv1846c/blaI

Normalized LFCs for Rv3413c/-:
(description and provenance of datasets)

Comparison of LFCs between selected condtions.

condition	Rv3413c/-	Rv1846c/blaI
Fe_supp_jason_reseq	-0.227	1.228
low_pH_jason_reseq	-1.228	-2.418
NO_jason_reseq	-0.223	0.189
B6_jason_reseq	-1.577	-1.843
MHCII_jason_reseq	0.184	0.355
Isoniazid02	0.045	0.901
Rifampicin4	-1.627	-1.267
Ethambutol3	-0.663	-0.326
Meropenem3	-1.381	0.204
Vancomycin16	-0.241	-0.796
Rv2680_day32	-2.448	-3.093
H37Rv_KO_MarP	-1.997	0.268
hypoxia_3wks	-1.101	0.271
hypoxia_6wks	-0.689	-1.37
glycerol	-1.463	-1.583
cholesterol	0.636	-1.124
AJ	-0.842	-2.04
Bibs02	0.376	-0.354
Bibs02c	0.45	1.129
BL6	-2.133	-3.872
BL6a	0.033	-0.525
BXD01	-2.613	-2.917
BXD010	-2.52	-4.379
BXD011	-1.682	-3.02
BXD03	-0.876	-2.664
BXD04	-1.737	-2.849
BXD05	-0.901	-1.847
BXD06	-2.441	-3.663
BXD07	-1.622	-3.87
BXD08	-0.919	-2.336
BXD09	-1.574	-3.237
CAST	-2.579	-2.636
CCcont	-1.116	-2.433
DS01	1.271	0.14
DS02	1.308	1.275
DS04	-0.483	-0.086
DS0c	0.685	-0.545
GP01	-0.639	-0.877
GP02	-1.205	-1.601
GP0c	-0.462	-1.516
NOD	0.623	-1.726
NZO	-1.272	-1.787
PWK	-1.398	-1.758
H37Rv_KO_CtpC	1.116	-2.732
H37Rv_KO_CtpD	-0.742	-2.466
H37Rv_KO_Rv1272	-1.022	-1.974
H37Rv_KO_SugABC	-0.023	-1.211
H37Rv_KO_MbtN	-1.244	-0.641
Trans05	-2.672	-2.346
macrophage_unactivated	-0.666	-0.073
IL1	0.056	-0.67
Rapamycin	0.921	-0.611
Tcell	-1.492	-1.613
GMCSF	1.212	0.972
IFNab	0.529	0.653
IFNg	-0.593	-1.235
IFNg_GMCSF1	-0.031	2.256
Rv1432_day32	-1.207	-0.632
Rv1565c_day32	-0.37	0.706
secA2_input	-0.249	-0.593
delta_Rv3594	0.329	0.22
delta_Rv3717	-0.038	0.052
delta_Rv3811	0.348	0.904
delta_Rv0954	0.39	0.249
PonA1	0.314	0.869
EccD1_KO	-1.069	0.908
EspI_KO	-0.248	0.279
PE35_KO	-0.627	-0.152
PPE68_KO	-0.448	0.07
glycerol2	-0.601	1.499
lignocerate	-0.392	0.168
oleate	-1.249	0.196
phosphatidylcholine	-0.524	0.0
acetate	1.252	0.0
glucAc	0.236	0.0
Rv0950ko	0.748	2.249
Rv1096ko	1.577	-0.175
Rv3684ko	0.278	1.621
delta_otsA_trehalose	-0.816	-0.429