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 Rv1700/-:
Show top 50 genes. Show bottom 10 genes with LOWEST correlation.

Most correlated genes.

update plot	correlation	link to info on gene
Rv1664/pks9	(cc=0.5246)	info on Rv1664/pks9
Rv0231/fadE4	(cc=0.5187)	info on Rv0231/fadE4
Rv3011c/gatA	(cc=0.513)	info on Rv3011c/gatA
Rv0999/-	(cc=0.5065)	info on Rv0999/-
Rv1551/plsB1	(cc=0.5005)	info on Rv1551/plsB1
Rv0469/umaA	(cc=0.4935)	info on Rv0469/umaA
Rv1533/-	(cc=0.49)	info on Rv1533/-
Rv0145/-	(cc=0.4883)	info on Rv0145/-
Rv3854c/ethA	(cc=0.4855)	info on Rv3854c/ethA
Rv1886c/fbpB	(cc=0.4772)	info on Rv1886c/fbpB

Correlation of Rv1700/- with Rv1664/pks9

Normalized LFCs for Rv1700/-:
(description and provenance of datasets)

Comparison of LFCs between selected condtions.

condition	Rv1700/-	Rv1664/pks9
Fe_supp_jason_reseq	0.464	0.611
low_pH_jason_reseq	-0.94	0.045
NO_jason_reseq	0.869	0.142
B6_jason_reseq	-1.811	-0.828
MHCII_jason_reseq	-1.595	-0.823
Isoniazid02	-0.217	-0.615
Rifampicin4	-2.905	0.317
Ethambutol3	-1.637	-0.916
Meropenem3	-2.016	-0.43
Vancomycin16	-1.711	-0.066
Rv2680_day32	-0.131	-0.348
H37Rv_KO_MarP	0.141	0.185
hypoxia_3wks	0.794	0.1
hypoxia_6wks	-0.616	-0.109
glycerol	-0.654	0.835
cholesterol	-0.216	0.203
AJ	0.0	-0.294
Bibs02	-0.775	-0.642
Bibs02c	-0.152	-0.735
BL6	-0.53	0.357
BL6a	0.133	0.426
BXD01	0.171	0.843
BXD010	-0.415	0.699
BXD011	0.167	0.761
BXD03	-0.573	0.258
BXD04	1.131	0.914
BXD05	0.0	1.375
BXD06	-0.311	0.775
BXD07	-0.448	0.961
BXD08	-0.431	0.75
BXD09	-0.328	0.524
CAST	-0.976	-0.215
CCcont	1.133	0.618
DS01	0.0	0.33
DS02	-0.325	0.246
DS04	-0.453	0.597
DS0c	-0.324	0.717
GP01	1.395	1.902
GP02	-0.353	-0.078
GP0c	1.552	0.564
NOD	-0.727	-0.21
NZO	0.892	-0.061
PWK	-0.142	-0.315
H37Rv_KO_CtpC	0.488	0.828
H37Rv_KO_CtpD	1.23	1.22
H37Rv_KO_Rv1272	0.693	1.456
H37Rv_KO_SugABC	0.962	1.39
H37Rv_KO_MbtN	0.31	0.294
Trans05	0.0	1.335
macrophage_unactivated	0.0	0.997
IL1	0.0	0.866
Rapamycin	-0.387	1.182
Tcell	0.375	1.105
GMCSF	0.0	1.017
IFNab	-0.381	0.955
IFNg	0.0	0.906
IFNg_GMCSF1	-0.396	0.525
Rv1432_day32	-0.632	-0.142
Rv1565c_day32	1.106	0.531
secA2_input	-0.714	-0.65
delta_Rv3594	-0.653	-0.311
delta_Rv3717	-0.959	-1.008
delta_Rv3811	-0.674	-0.47
delta_Rv0954	0.116	-0.74
PonA1	-0.278	-0.744
EccD1_KO	-1.253	-0.549
EspI_KO	-2.176	-0.935
PE35_KO	-0.828	-0.563
PPE68_KO	-0.166	-0.454
glycerol2	-0.95	-0.862
lignocerate	-1.371	-0.721
oleate	-0.274	-0.364
phosphatidylcholine	-0.639	-0.623
acetate	-0.437	-0.806
glucAc	-2.067	-0.808
Rv0950ko	0.09	-0.371
Rv1096ko	-0.287	0.277
Rv3684ko	0.386	-0.665
delta_otsA_trehalose	-0.885	1.396