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 Rv1845c/blaR:

update plot	correlation	link to info on gene
Rv3645/-	(cc=0.5428)	info on Rv3645/-
Rv2207/cobT	(cc=0.5397)	info on Rv2207/cobT
Rv1458c/-	(cc=0.4975)	info on Rv1458c/-
Rv1349/irtB	(cc=0.4542)	info on Rv1349/irtB
Rv1081c/-	(cc=0.4414)	info on Rv1081c/-
Rv3446c/-	(cc=0.4167)	info on Rv3446c/-
Rv1692/-	(cc=0.4155)	info on Rv1692/-
Rv1308/atpA	(cc=0.4149)	info on Rv1308/atpA
Rv1534/-	(cc=0.4056)	info on Rv1534/-
Rv3776/-	(cc=0.4001)	info on Rv3776/-

Correlation of Rv1845c/blaR with Rv1349/irtB

Normalized LFCs for Rv1845c/blaR:
(description and provenance of datasets)

	Rv1845c/blaR	Rv1349/irtB
Fe_supp_jason_reseq	1.796	1.847
low_pH_jason_reseq	6.0	2.844
NO_jason_reseq	0.0	-0.69
B6_jason_reseq	0.0	-0.292
MHCII_jason_reseq	0.0	-0.257
Isoniazid02	0.0	-0.201
Rifampicin4	0.0	-0.374
Ethambutol3	0.0	-0.168
Meropenem3	0.0	-0.165
Vancomycin16	0.0	-0.366
Rv2680_day32	0.0	-0.131
H37Rv_KO_MarP	0.961	-0.586
hypoxia_3wks	0.0	-0.55
hypoxia_6wks	0.0	0.0
glycerol	1.24	-0.856
cholesterol	0.0	-0.614
AJ	0.0	-0.983
Bibs02	0.0	-0.273
Bibs02c	0.0	-0.887
BL6	0.0	-0.53
BL6a	0.0	-0.839
BXD01	0.13	-0.552
BXD010	0.0	-0.543
BXD011	0.0	-0.412
BXD03	0.0	-0.573
BXD04	0.0	-0.4
BXD05	0.0	-0.57
BXD06	0.254	-0.566
BXD07	0.0	-0.587
BXD08	0.0	-0.564
BXD09	0.0	-0.596
CAST	0.0	-0.537
CCcont	0.285	0.196
DS01	0.0	0.0
DS02	0.217	1.251
DS04	0.37	-0.453
DS0c	0.0	0.0
GP01	0.099	-0.418
GP02	0.0	-0.353
GP0c	0.357	-0.551
NOD	0.0	-0.524
NZO	0.0	-0.465
PWK	0.0	-0.831
H37Rv_KO_CtpC	0.162	-0.379
H37Rv_KO_CtpD	0.918	-0.41
H37Rv_KO_Rv1272	0.0	-0.598
H37Rv_KO_SugABC	0.099	-0.231
H37Rv_KO_MbtN	0.943	-0.154
Trans05	0.0	-0.423
macrophage_unactivated	0.0	-0.436
IL1	0.0	0.374
Rapamycin	0.0	0.0
Tcell	0.0	0.0
GMCSF	0.0	-0.364
IFNab	0.0	-0.417
IFNg	0.0	-0.369
IFNg_GMCSF1	0.0	-0.434
Rv1432_day32	0.0	-0.18
Rv1565c_day32	0.0	0.0
secA2_input	3.034	-1.061
delta_Rv3594	-1.319	-1.436
delta_Rv3717	-0.927	-1.339
delta_Rv3811	-1.096	-1.224
delta_Rv0954	-0.196	-0.083
PonA1	2.086	0.792
EccD1_KO	0.77	-1.121
EspI_KO	0.667	-0.973
PE35_KO	-1.467	0.983
PPE68_KO	-0.579	-0.25
glycerol2	0.0	-1.153
lignocerate	0.0	-1.296
oleate	0.0	-1.704
phosphatidylcholine	0.0	-1.153
acetate	0.0	-1.368
glucAc	0.0	-1.1
Rv0950ko	-0.844	-0.844
Rv1096ko	-0.546	0.483
Rv3684ko	2.184	-0.593
delta_otsA_trehalose	-4.196	-0.881