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 Rv3829c/-:

update plot	correlation	link to info on gene
Rv3108/-	(cc=0.5668)	info on Rv3108/-
Rv1946c/lppG	(cc=0.545)	info on Rv1946c/lppG
Rv3398c/idsA1	(cc=0.5255)	info on Rv3398c/idsA1
Rv0844c/narL	(cc=0.5092)	info on Rv0844c/narL
Rv2452c/-	(cc=0.5074)	info on Rv2452c/-
Rv2807/-	(cc=0.4958)	info on Rv2807/-
Rv2428/ahpC	(cc=0.4923)	info on Rv2428/ahpC
Rv2070c/cobK	(cc=0.4855)	info on Rv2070c/cobK
Rv3166c/-	(cc=0.4773)	info on Rv3166c/-
Rv1962A/vapB35	(cc=0.4712)	info on Rv1962A/vapB35

Correlation of Rv3829c/- with Rv3166c/-

Normalized LFCs for Rv3829c/-:
(description and provenance of datasets)

	Rv3829c/-	Rv3166c/-
Fe_supp_jason_reseq	-0.511	1.028
low_pH_jason_reseq	0.555	0.482
NO_jason_reseq	-0.27	0.087
B6_jason_reseq	-1.185	-1.11
MHCII_jason_reseq	-0.647	-0.193
Isoniazid02	-0.31	0.412
Rifampicin4	-0.523	-0.073
Ethambutol3	-0.102	0.501
Meropenem3	0.125	0.214
Vancomycin16	-0.072	0.21
Rv2680_day32	0.917	0.781
H37Rv_KO_MarP	0.27	0.183
hypoxia_3wks	-0.419	0.0
hypoxia_6wks	-0.737	-0.336
glycerol	0.336	0.803
cholesterol	-0.012	0.497
AJ	0.113	0.861
Bibs02	-0.907	-0.621
Bibs02c	-0.161	1.303
BL6	0.639	1.769
BL6a	0.288	2.045
BXD01	0.542	1.207
BXD010	0.608	0.811
BXD011	0.34	1.128
BXD03	0.378	1.462
BXD04	0.534	1.549
BXD05	-0.033	1.91
BXD06	0.398	1.378
BXD07	0.361	1.851
BXD08	0.725	1.11
BXD09	0.225	1.744
CAST	-0.39	-0.284
CCcont	0.446	1.322
DS01	-0.332	0.219
DS02	0.254	0.277
DS04	-0.547	0.28
DS0c	0.071	0.082
GP01	0.313	-0.079
GP02	0.762	1.205
GP0c	-0.438	0.694
NOD	0.643	1.009
NZO	-0.189	-0.525
PWK	-0.729	-1.138
H37Rv_KO_CtpC	0.282	1.129
H37Rv_KO_CtpD	1.268	2.225
H37Rv_KO_Rv1272	0.713	0.296
H37Rv_KO_SugABC	0.807	0.159
H37Rv_KO_MbtN	0.201	-0.22
Trans05	0.255	0.097
macrophage_unactivated	0.47	0.71
IL1	0.605	0.86
Rapamycin	0.218	1.019
Tcell	0.362	0.248
GMCSF	1.117	0.158
IFNab	0.726	1.128
IFNg	0.593	0.115
IFNg_GMCSF1	0.097	1.439
Rv1432_day32	0.387	0.931
Rv1565c_day32	0.441	0.035
secA2_input	0.313	-0.233
delta_Rv3594	-0.381	0.537
delta_Rv3717	-0.58	-0.866
delta_Rv3811	0.22	-0.235
delta_Rv0954	0.013	-0.544
PonA1	0.149	-0.922
EccD1_KO	1.207	0.533
EspI_KO	1.149	0.639
PE35_KO	1.254	0.359
PPE68_KO	1.318	0.266
glycerol2	-0.441	-0.319
lignocerate	-0.106	0.222
oleate	-0.225	-0.323
phosphatidylcholine	-0.409	0.088
acetate	-0.447	0.53
glucAc	-0.338	0.233
Rv0950ko	-0.347	-1.101
Rv1096ko	0.205	-1.143
Rv3684ko	-0.236	-0.789
delta_otsA_trehalose	-0.033	-0.826