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 Rv3509c/ilvX:

update plot	correlation	link to info on gene
Rv0578c/PE_PGRS7	(cc=0.6284)	info on Rv0578c/PE_PGRS7
Rv0218/-	(cc=0.5765)	info on Rv0218/-
Rv3624c/hpt	(cc=0.5668)	info on Rv3624c/hpt
Rv3344c/PE_PGRS49	(cc=0.5628)	info on Rv3344c/PE_PGRS49
Rv2841c/nusA	(cc=0.5514)	info on Rv2841c/nusA
Rv1135c/PPE16	(cc=0.5487)	info on Rv1135c/PPE16
Rv3607c/folB	(cc=0.5436)	info on Rv3607c/folB
Rv0835/lpqQ	(cc=0.5344)	info on Rv0835/lpqQ
Rv1734c/-	(cc=0.5338)	info on Rv1734c/-
Rv2571c/-	(cc=0.5323)	info on Rv2571c/-

Correlation of Rv3509c/ilvX with Rv2841c/nusA

Normalized LFCs for Rv3509c/ilvX:
(description and provenance of datasets)

	Rv3509c/ilvX	Rv2841c/nusA
Fe_supp_jason_reseq	-0.081	0.0
low_pH_jason_reseq	-0.375	0.0
NO_jason_reseq	-0.257	0.0
B6_jason_reseq	0.367	0.0
MHCII_jason_reseq	0.362	0.0
Isoniazid02	1.147	-0.201
Rifampicin4	0.55	0.0
Ethambutol3	0.899	0.423
Meropenem3	0.328	-0.165
Vancomycin16	0.727	0.0
Rv2680_day32	-0.207	0.0
H37Rv_KO_MarP	0.302	0.0
hypoxia_3wks	-0.104	0.0
hypoxia_6wks	-0.355	0.0
glycerol	0.699	0.202
cholesterol	0.869	0.509
AJ	0.282	0.0
Bibs02	0.34	0.0
Bibs02c	0.45	0.0
BL6	0.502	0.0
BL6a	0.458	0.0
BXD01	0.516	0.0
BXD010	0.03	0.0
BXD011	0.68	0.0
BXD03	0.047	0.0
BXD04	0.408	0.0
BXD05	-0.064	0.0
BXD06	0.39	0.0
BXD07	0.174	0.0
BXD08	-0.011	0.0
BXD09	0.126	0.0
CAST	0.207	0.439
CCcont	-0.281	0.0
DS01	0.409	0.83
DS02	0.28	0.0
DS04	0.835	0.0
DS0c	0.594	0.0
GP01	-0.119	0.0
GP02	-0.02	0.0
GP0c	-0.314	0.0
NOD	0.714	0.225
NZO	-0.048	0.0
PWK	0.415	0.0
H37Rv_KO_CtpC	-0.006	0.571
H37Rv_KO_CtpD	0.044	0.0
H37Rv_KO_Rv1272	0.167	0.0
H37Rv_KO_SugABC	0.471	0.0
H37Rv_KO_MbtN	0.257	0.103
Trans05	0.094	0.131
macrophage_unactivated	-0.732	-2.14
IL1	-0.602	-2.011
Rapamycin	-0.868	-2.081
Tcell	-0.459	-2.209
GMCSF	-0.428	-1.79
IFNab	-0.856	-2.05
IFNg	-0.877	-1.812
IFNg_GMCSF1	0.226	-2.13
Rv1432_day32	0.756	-1.124
Rv1565c_day32	0.175	0.0
secA2_input	-0.189	-0.216
delta_Rv3594	0.783	0.742
delta_Rv3717	0.039	0.736
delta_Rv3811	0.651	1.261
delta_Rv0954	0.915	0.178
PonA1	0.743	0.0
EccD1_KO	0.072	-0.595
EspI_KO	-0.125	-0.799
PE35_KO	-0.064	-0.817
PPE68_KO	-0.384	-0.896
glycerol2	-0.174	0.0
lignocerate	-0.358	0.0
oleate	-0.33	0.0
phosphatidylcholine	-0.209	0.0
acetate	-0.849	0.0
glucAc	-0.171	0.0
Rv0950ko	0.612	0.727
Rv1096ko	0.953	0.727
Rv3684ko	0.4	1.772
delta_otsA_trehalose	-0.209	0.133