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 Rv3656c/-:

update plot	correlation	link to info on gene
Rv1604/impA	(cc=0.5376)	info on Rv1604/impA
Rv1583c/-	(cc=0.493)	info on Rv1583c/-
Rv3819/-	(cc=0.4831)	info on Rv3819/-
Rv2253/-	(cc=0.4715)	info on Rv2253/-
Rv2689c/-	(cc=0.4707)	info on Rv2689c/-
Rv3470c/ilvB2	(cc=0.4619)	info on Rv3470c/ilvB2
Rv0698/-	(cc=0.4599)	info on Rv0698/-
Rv2665/-	(cc=0.4531)	info on Rv2665/-
Rv1366/-	(cc=0.4479)	info on Rv1366/-
Rv3904c/esxE	(cc=0.4475)	info on Rv3904c/esxE

Correlation of Rv3656c/- with Rv3904c/esxE

Normalized LFCs for Rv3656c/-:
(description and provenance of datasets)

	Rv3656c/-	Rv3904c/esxE
Fe_supp_jason_reseq	-1.424	-0.758
low_pH_jason_reseq	-0.294	1.2
NO_jason_reseq	-1.179	-0.218
B6_jason_reseq	-3.075	-1.498
MHCII_jason_reseq	-0.951	-2.38
Isoniazid02	-0.317	0.581
Rifampicin4	0.374	-0.969
Ethambutol3	-0.128	0.923
Meropenem3	-0.182	0.589
Vancomycin16	0.26	0.621
Rv2680_day32	-0.461	0.663
H37Rv_KO_MarP	0.099	0.282
hypoxia_3wks	-0.443	-1.707
hypoxia_6wks	-1.006	-1.518
glycerol	-0.094	-1.878
cholesterol	-0.102	-0.598
AJ	0.684	0.94
Bibs02	-0.416	0.415
Bibs02c	-0.252	-3.519
BL6	1.337	1.499
BL6a	0.0	0.247
BXD01	1.029	1.02
BXD010	0.581	1.327
BXD011	0.736	1.124
BXD03	0.445	1.066
BXD04	-0.117	0.649
BXD05	0.225	0.256
BXD06	0.0	1.025
BXD07	1.109	1.127
BXD08	0.392	0.963
BXD09	0.18	0.59
CAST	0.976	0.48
CCcont	1.844	2.066
DS01	0.441	-0.65
DS02	-0.101	0.047
DS04	0.991	1.539
DS0c	-2.696	-1.281
GP01	0.448	1.039
GP02	-0.316	0.621
GP0c	0.531	0.977
NOD	-0.387	-1.04
NZO	4.004	2.724
PWK	0.612	-0.021
H37Rv_KO_CtpC	0.072	2.394
H37Rv_KO_CtpD	1.582	1.81
H37Rv_KO_Rv1272	-0.535	1.614
H37Rv_KO_SugABC	-0.763	2.885
H37Rv_KO_MbtN	0.046	1.519
Trans05	-0.539	2.42
macrophage_unactivated	0.369	-0.937
IL1	-1.172	-0.51
Rapamycin	-1.05	-0.829
Tcell	-0.342	-2.102
GMCSF	-0.517	-0.713
IFNab	-0.662	-1.569
IFNg	-0.649	-0.775
IFNg_GMCSF1	-1.411	-1.581
Rv1432_day32	0.343	0.485
Rv1565c_day32	0.377	0.25
secA2_input	-0.421	1.943
delta_Rv3594	-1.473	0.15
delta_Rv3717	-1.013	-0.711
delta_Rv3811	-0.207	-0.648
delta_Rv0954	-0.916	0.411
PonA1	0.166	0.32
EccD1_KO	-0.638	-0.842
EspI_KO	0.034	0.704
PE35_KO	0.172	0.7
PPE68_KO	0.618	0.192
glycerol2	0.465	-0.43
lignocerate	1.137	-0.537
oleate	-0.167	-0.834
phosphatidylcholine	0.604	-0.556
acetate	0.509	-0.045
glucAc	2.591	-0.352
Rv0950ko	0.458	1.36
Rv1096ko	0.805	0.772
Rv3684ko	0.616	0.167
delta_otsA_trehalose	0.629	4.617