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 Rv2962c/-:

update plot	correlation	link to info on gene
Rv1866/-	(cc=0.5811)	info on Rv1866/-
Rv3223c/sigH	(cc=0.5099)	info on Rv3223c/sigH
Rv3555c/-	(cc=0.4758)	info on Rv3555c/-
Rv1755c/plcD	(cc=0.4722)	info on Rv1755c/plcD
Rv1872c/lldD2	(cc=0.4636)	info on Rv1872c/lldD2
Rv1913/-	(cc=0.4592)	info on Rv1913/-
Rv3110/moaB1	(cc=0.4558)	info on Rv3110/moaB1
Rv1087/PE_PGRS21	(cc=0.4554)	info on Rv1087/PE_PGRS21
Rv2841c/nusA	(cc=0.4546)	info on Rv2841c/nusA
Rv1962A/vapB35	(cc=0.4544)	info on Rv1962A/vapB35

Correlation of Rv2962c/- with Rv1872c/lldD2

Normalized LFCs for Rv2962c/-:
(description and provenance of datasets)

	Rv2962c/-	Rv1872c/lldD2
Fe_supp_jason_reseq	0.655	0.493
low_pH_jason_reseq	-0.823	-0.893
NO_jason_reseq	-0.142	-0.971
B6_jason_reseq	0.103	-1.228
MHCII_jason_reseq	0.459	-1.417
Isoniazid02	1.398	0.418
Rifampicin4	-0.192	-0.114
Ethambutol3	1.025	0.854
Meropenem3	-0.193	0.158
Vancomycin16	-0.326	0.48
Rv2680_day32	0.05	-0.449
H37Rv_KO_MarP	0.586	-0.591
hypoxia_3wks	0.239	1.12
hypoxia_6wks	0.056	1.533
glycerol	-0.984	1.369
cholesterol	1.795	0.764
AJ	0.35	0.062
Bibs02	-0.351	-0.285
Bibs02c	-0.606	-0.634
BL6	1.034	0.128
BL6a	0.026	-0.296
BXD01	0.577	0.164
BXD010	0.626	0.54
BXD011	0.111	0.304
BXD03	0.396	0.252
BXD04	0.461	0.208
BXD05	0.203	1.003
BXD06	0.331	0.469
BXD07	0.504	0.575
BXD08	0.514	0.478
BXD09	0.362	0.318
CAST	-0.235	-1.313
CCcont	0.57	0.04
DS01	0.248	-1.098
DS02	0.176	0.871
DS04	-0.013	0.0
DS0c	0.163	-0.22
GP01	0.759	-0.021
GP02	1.286	-0.764
GP0c	0.698	0.442
NOD	0.732	-0.35
NZO	0.026	-0.273
PWK	0.148	-0.355
H37Rv_KO_CtpC	0.459	1.363
H37Rv_KO_CtpD	1.486	0.774
H37Rv_KO_Rv1272	0.532	1.259
H37Rv_KO_SugABC	0.535	1.162
H37Rv_KO_MbtN	1.092	0.564
Trans05	0.78	0.414
macrophage_unactivated	-0.18	-1.515
IL1	-0.878	-2.928
Rapamycin	-1.004	-2.056
Tcell	-0.583	-5.002
GMCSF	-1.075	-1.935
IFNab	-0.626	2.174
IFNg	-0.831	-6.0
IFNg_GMCSF1	-0.65	-5.247
Rv1432_day32	0.159	-0.468
Rv1565c_day32	0.047	-0.224
secA2_input	-0.576	1.312
delta_Rv3594	0.113	-0.153
delta_Rv3717	-0.036	-0.389
delta_Rv3811	0.11	-0.225
delta_Rv0954	0.554	-0.6
PonA1	-0.022	-0.697
EccD1_KO	0.832	1.141
EspI_KO	-0.086	0.388
PE35_KO	0.615	0.747
PPE68_KO	0.563	0.326
glycerol2	0.397	0.301
lignocerate	0.189	-0.276
oleate	0.238	0.899
phosphatidylcholine	0.321	0.342
acetate	0.268	-1.189
glucAc	0.346	-0.983
Rv0950ko	-0.169	-0.051
Rv1096ko	0.229	-0.772
Rv3684ko	0.416	-0.891
delta_otsA_trehalose	1.239	1.781