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Motif Scan

Transcription Factor binding motifs are commonly found enriched in cis-regulatory elements and can inform the potential regulatory mechanism of the elements. The first step to study these DNA motifs is to scan their occurence in the genome regions.

The Default MotifSet

Currently, the motif scan function uses a default motif dataset that contains >2000 motifs from three databases [Khan et al., 2018, Kulakovskiy et al., 2018, Jolma et al., 2013], each motif is also annotated with human and mouse gene names to facilitate further interpretation.

Following the analysis in [Vierstra et al., 2020] (see also this great blog), these motifs are clustered into 286 motif-clusters based on their similarity (and some motifs are almost identical). We will scan all individual motifs here, but also aggregate the results to motif-cluster level. It is recommended to perform futher analysis at the motif-cluster level (such as motif enrichment analysis).

from ALLCools.mcds import RegionDS
from ALLCools.motif import MotifSet, get_default_motif_set

# check out the default motif set
default_motif_set = get_default_motif_set()
default_motif_set.n_motifs

2179

# metadata of the motifs
default_motif_set.meta_table

	human_genes	mouse_genes	cluster_id	database	concensus	relative_orientation	width	left_offset	right_offset
motif
LHX6_homeodomain_3	LHX6	Lhx6	c1	Taipale_Cell_2013	TGATTGCAATCA	Positive	12	0	0
Lhx8.mouse_homeodomain_3	LHX8	Lhx8	c1	Taipale_Cell_2013	TGATTGCAATTA	Negative	12	0	0
LHX2_MOUSE.H11MO.0.A	LHX2	Lhx2	c2	HOCOMOCO_v11	ACTAATTAAC	Negative	10	7	9
LHX2_HUMAN.H11MO.0.A	LHX2	Lhx2	c2	HOCOMOCO_v11	AACTAATTAAAA	Negative	12	6	8
LHX3_MOUSE.H11MO.0.C	LHX3	Lhx3	c2	HOCOMOCO_v11	TTAATTAGC	Negative	9	8	9
...	...	...	...	...	...	...	...	...	...
Ahr+Arnt_MA0006.1	AMT	Amt	c284	Jaspar2018	TGCGTG	Positive	6	2	1
KLF8_HUMAN.H11MO.0.C	KLF8	Klf8	c285	HOCOMOCO_v11	CAGGGGGTG	Positive	9	0	0
KLF8_MOUSE.H11MO.0.C	KLF8	Klf8	c285	HOCOMOCO_v11	CAGGGGGTG	Positive	9	0	0
ZSCAN4_MA1155.1	ZSCAN4	Zscan4b	c286	Jaspar2018	TGCACACACTGAAAA	Positive	15	0	0
ZSCAN4_C2H2_1	ZSCAN4	Zscan4b	c286	Taipale_Cell_2013	TGCACACACTGAAAA	Positive	15	0	0

2220 rows × 9 columns

# motif cluster
default_motif_set.motif_cluster

motif
LHX6_homeodomain_3            c1
Lhx8.mouse_homeodomain_3      c1
LHX2_MOUSE.H11MO.0.A          c2
LHX2_HUMAN.H11MO.0.A          c2
LHX3_MOUSE.H11MO.0.C          c2
                            ... 
Ahr+Arnt_MA0006.1           c284
KLF8_HUMAN.H11MO.0.C        c285
KLF8_MOUSE.H11MO.0.C        c285
ZSCAN4_MA1155.1             c286
ZSCAN4_C2H2_1               c286
Length: 2174, dtype: object

# single motif object
default_motif_set.motif_list[0]

<ALLCools.motif.motifs.Motif at 0x7f1bbc8c4730>

Motif PSSM Cutoffs

# To re-calculate motif thresholds with a different method or parameter

# default_motif_set.calculate_threshold(method='balanced', cpu=1, threshold_value=1000)

Scan Default Motifs

dmr_ds = RegionDS.open('test_HIP', select_dir=['dmr'])
dmr_ds

Using dmr as region_dim

<xarray.RegionDS>
Dimensions:              (count_type: 2, dmr: 132, sample: 20, sample_collapsed: 10)
Coordinates:
  * count_type           (count_type) <U3 'mc' 'cov'
  * dmr                  (dmr) <U9 'chr1-0' 'chr1-1' ... 'chr19-122' 'chr19-123'
    dmr_chrom            (dmr) <U5 'chr1' 'chr1' 'chr1' ... 'chr19' 'chr19'
    dmr_end              (dmr) int64 10002172 10003542 ... 5099203 5099952
    dmr_length           (dmr) int64 2 305 54 2 2 2 ... 924 632 842 195 399 335
    dmr_ndms             (dmr) int64 1 7 2 1 1 1 1 13 3 ... 2 7 13 19 9 9 3 6 13
    dmr_start            (dmr) int64 10002170 10003237 ... 5098804 5099617
  * sample               (sample) <U18 'snm3C_ASC' 'snm3C_CA1' ... 'snmC_OPC'
  * sample_collapsed     (sample_collapsed) object 'ASC' 'CA1' ... 'ODC' 'OPC'
Data variables:
    dmr_da               (sample, dmr, count_type) uint32 4294967295 ... 4294...
    dmr_da_frac          (sample, dmr) float32 1.0 1.0 1.0 1.0 ... 1.0 1.0 1.0
    dmr_state            (sample, dmr) int8 -1 0 0 1 -1 -1 -1 ... 0 0 0 0 0 0 0
    dmr_state_collapsed  (dmr, sample_collapsed) int8 0 0 0 0 0 0 ... 0 0 0 0 0
Attributes:
    chrom_size_path:     /home/hanliu/pkg/ALLCools_pycharm/docs/allcools/clus...
    region_dim:          dmr
    region_ds_location:  /home/hanliu/pkg/ALLCools_pycharm/docs/allcools/clus...

xarray.RegionDS

• Dimensions:
  • count_type: 2
  • dmr: 132
  • sample: 20
  • sample_collapsed: 10
• Coordinates: (9)
  • count_type
    (count_type)
    <U3
    'mc' 'cov'

    array(['mc', 'cov'], dtype='<U3')

  • dmr
    (dmr)
    <U9
    'chr1-0' 'chr1-1' ... 'chr19-123'

    array(['chr1-0', 'chr1-1', 'chr1-2', 'chr1-3', 'chr1-4', 'chr1-5', 'chr1-6',
           'chr1-7', 'chr19-0', 'chr19-1', 'chr19-2', 'chr19-3', 'chr19-4',
           'chr19-5', 'chr19-6', 'chr19-7', 'chr19-8', 'chr19-9', 'chr19-10',
           'chr19-11', 'chr19-12', 'chr19-13', 'chr19-14', 'chr19-15', 'chr19-16',
           'chr19-17', 'chr19-18', 'chr19-19', 'chr19-20', 'chr19-21', 'chr19-22',
           'chr19-23', 'chr19-24', 'chr19-25', 'chr19-26', 'chr19-27', 'chr19-28',
           'chr19-29', 'chr19-30', 'chr19-31', 'chr19-32', 'chr19-33', 'chr19-34',
           'chr19-35', 'chr19-36', 'chr19-37', 'chr19-38', 'chr19-39', 'chr19-40',
           'chr19-41', 'chr19-42', 'chr19-43', 'chr19-44', 'chr19-45', 'chr19-46',
           'chr19-47', 'chr19-48', 'chr19-49', 'chr19-50', 'chr19-51', 'chr19-52',
           'chr19-53', 'chr19-54', 'chr19-55', 'chr19-56', 'chr19-57', 'chr19-58',
           'chr19-59', 'chr19-60', 'chr19-61', 'chr19-62', 'chr19-63', 'chr19-64',
           'chr19-65', 'chr19-66', 'chr19-67', 'chr19-68', 'chr19-69', 'chr19-70',
           'chr19-71', 'chr19-72', 'chr19-73', 'chr19-74', 'chr19-75', 'chr19-76',
           'chr19-77', 'chr19-78', 'chr19-79', 'chr19-80', 'chr19-81', 'chr19-82',
           'chr19-83', 'chr19-84', 'chr19-85', 'chr19-86', 'chr19-87', 'chr19-88',
           'chr19-89', 'chr19-90', 'chr19-91', 'chr19-92', 'chr19-93', 'chr19-94',
           'chr19-95', 'chr19-96', 'chr19-97', 'chr19-98', 'chr19-99', 'chr19-100',
           'chr19-101', 'chr19-102', 'chr19-103', 'chr19-104', 'chr19-105',
           'chr19-106', 'chr19-107', 'chr19-108', 'chr19-109', 'chr19-110',
           'chr19-111', 'chr19-112', 'chr19-113', 'chr19-114', 'chr19-115',
           'chr19-116', 'chr19-117', 'chr19-118', 'chr19-119', 'chr19-120',
           'chr19-121', 'chr19-122', 'chr19-123'], dtype='<U9')

  • dmr_chrom
    (dmr)
    <U5
    'chr1' 'chr1' ... 'chr19' 'chr19'

    array(['chr1', 'chr1', 'chr1', 'chr1', 'chr1', 'chr1', 'chr1', 'chr1',
           'chr19', 'chr19', 'chr19', 'chr19', 'chr19', 'chr19', 'chr19',
           'chr19', 'chr19', 'chr19', 'chr19', 'chr19', 'chr19', 'chr19',
           'chr19', 'chr19', 'chr19', 'chr19', 'chr19', 'chr19', 'chr19',
           'chr19', 'chr19', 'chr19', 'chr19', 'chr19', 'chr19', 'chr19',
           'chr19', 'chr19', 'chr19', 'chr19', 'chr19', 'chr19', 'chr19',
           'chr19', 'chr19', 'chr19', 'chr19', 'chr19', 'chr19', 'chr19',
           'chr19', 'chr19', 'chr19', 'chr19', 'chr19', 'chr19', 'chr19',
           'chr19', 'chr19', 'chr19', 'chr19', 'chr19', 'chr19', 'chr19',
           'chr19', 'chr19', 'chr19', 'chr19', 'chr19', 'chr19', 'chr19',
           'chr19', 'chr19', 'chr19', 'chr19', 'chr19', 'chr19', 'chr19',
           'chr19', 'chr19', 'chr19', 'chr19', 'chr19', 'chr19', 'chr19',
           'chr19', 'chr19', 'chr19', 'chr19', 'chr19', 'chr19', 'chr19',
           'chr19', 'chr19', 'chr19', 'chr19', 'chr19', 'chr19', 'chr19',
           'chr19', 'chr19', 'chr19', 'chr19', 'chr19', 'chr19', 'chr19',
           'chr19', 'chr19', 'chr19', 'chr19', 'chr19', 'chr19', 'chr19',
           'chr19', 'chr19', 'chr19', 'chr19', 'chr19', 'chr19', 'chr19',
           'chr19', 'chr19', 'chr19', 'chr19', 'chr19', 'chr19', 'chr19',
           'chr19', 'chr19', 'chr19', 'chr19', 'chr19'], dtype='<U5')

  • dmr_end
    (dmr)
    int64
    10002172 10003542 ... 5099952

    array([10002172, 10003542, 10003967, 10005479, 10007099, 10007758,
           10008881, 10009927,  5000194,  5000343,  5000715,  5001506,
            5001549,  5003862,  5004785,  5005319,  5005816,  5006789,
            5008015,  5008084,  5008130,  5008805,  5010091,  5011268,
            5011724,  5011926,  5012429,  5012955,  5013312,  5013603,
            5014250,  5014562,  5014921,  5015099,  5016145,  5016791,
            5017181,  5017656,  5018165,  5018340,  5019014,  5019656,
            5020498,  5021894,  5022034,  5022299,  5023452,  5025645,
            5026013,  5026581,  5028070,  5029223,  5029469,  5029930,
            5031623,  5032343,  5033665,  5035273,  5036180,  5036656,
            5037800,  5040294,  5040872,  5042216,  5042541,  5043207,
            5043818,  5045206,  5046083,  5046469,  5047139,  5050164,
            5051764,  5054110,  5055419,  5056089,  5056189,  5056309,
            5056642,  5057152,  5057233,  5059280,  5059541,  5060286,
            5060636,  5061033,  5061586,  5062181,  5062652,  5063270,
            5064727,  5065461,  5065765,  5066074,  5066405,  5067916,
            5069149,  5070132,  5071656,  5071800,  5073983,  5074921,
            5076037,  5076379,  5077207,  5078490,  5078805,  5080040,
            5080229,  5081032,  5081240,  5081796,  5082893,  5083285,
            5083313,  5083586,  5084274,  5084686,  5086323,  5087101,
            5087539,  5089466,  5089734,  5090283,  5091820,  5092737,
            5094022,  5095601,  5097380,  5097870,  5099203,  5099952])

  • dmr_length
    (dmr)
    int64
    2 305 54 2 2 ... 842 195 399 335

    array([   2,  305,   54,    2,    2,    2,    2,  440,  171,   12,    2,
              2,   22,  504,  128,  146,  201,    2,    2,    2,    2,  182,
              2,  246,    2,    2,  101,  343,   49,  183,    2,   88,    2,
              2,   89,  385,   55,    2,    2,   48,  144,    2,    2,  821,
              2,    2,  306,  913,    2,   71,   91,   22,   21,  149,    2,
              2,    2,    2,   57,   76,    2,  532,  552,  211,    2,  243,
              2,    2,  322,   63,    2, 2314, 1029, 2090,    2,   58,    2,
             67,    2,  253,    2, 1351,    2,  478,    2,  127,   42,   43,
              2,   46,    2,  482,   14,    2,    2,  773,  760,    2,  661,
            126,  345,  687,  537,    2,  469,  866,    2,    2,   59,  315,
              2,  368, 1053,  367,    2,    2,  186,    2,  391,  108,  323,
             31,    2,  138,  434,  589,  924,  632,  842,  195,  399,  335])

  • dmr_ndms
    (dmr)
    int64
    1 7 2 1 1 1 1 ... 13 19 9 9 3 6 13

    array([ 1,  7,  2,  1,  1,  1,  1, 13,  3,  2,  1,  1,  2,  5,  2,  3,  2,
            1,  1,  1,  1,  4,  1,  2,  1,  1,  3,  6,  4,  3,  1,  4,  1,  1,
            3,  7,  4,  1,  1,  2,  4,  1,  1,  8,  1,  1,  9, 14,  1,  5,  3,
            2,  2,  2,  1,  1,  1,  1,  2,  2,  1, 17, 11,  3,  1,  5,  1,  1,
            9,  4,  1, 33, 28, 56,  1,  2,  1,  2,  1,  4,  1, 20,  1,  7,  1,
            2,  2,  2,  1,  2,  1,  7,  3,  1,  1, 15, 29,  1, 20,  4,  8, 13,
            4,  1,  5, 15,  1,  1,  4,  6,  1, 10, 47,  9,  1,  1,  2,  1,  3,
            4,  8,  2,  1,  2,  7, 13, 19,  9,  9,  3,  6, 13])

  • dmr_start
    (dmr)
    int64
    10002170 10003237 ... 5099617

    array([10002170, 10003237, 10003913, 10005477, 10007097, 10007756,
           10008879, 10009487,  5000023,  5000331,  5000713,  5001504,
            5001527,  5003358,  5004657,  5005173,  5005615,  5006787,
            5008013,  5008082,  5008128,  5008623,  5010089,  5011022,
            5011722,  5011924,  5012328,  5012612,  5013263,  5013420,
            5014248,  5014474,  5014919,  5015097,  5016056,  5016406,
            5017126,  5017654,  5018163,  5018292,  5018870,  5019654,
            5020496,  5021073,  5022032,  5022297,  5023146,  5024732,
            5026011,  5026510,  5027979,  5029201,  5029448,  5029781,
            5031621,  5032341,  5033663,  5035271,  5036123,  5036580,
            5037798,  5039762,  5040320,  5042005,  5042539,  5042964,
            5043816,  5045204,  5045761,  5046406,  5047137,  5047850,
            5050735,  5052020,  5055417,  5056031,  5056187,  5056242,
            5056640,  5056899,  5057231,  5057929,  5059539,  5059808,
            5060634,  5060906,  5061544,  5062138,  5062650,  5063224,
            5064725,  5064979,  5065751,  5066072,  5066403,  5067143,
            5068389,  5070130,  5070995,  5071674,  5073638,  5074234,
            5075500,  5076377,  5076738,  5077624,  5078803,  5080038,
            5080170,  5080717,  5081238,  5081428,  5081840,  5082918,
            5083311,  5083584,  5084088,  5084684,  5085932,  5086993,
            5087216,  5089435,  5089732,  5090145,  5091386,  5092148,
            5093098,  5094969,  5096538,  5097675,  5098804,  5099617])

  • sample
    (sample)
    <U18
    'snm3C_ASC' ... 'snmC_OPC'

    array(['snm3C_ASC', 'snm3C_CA1', 'snm3C_CA23', 'snm3C_CGE-VipLamp5',
           'snm3C_DG', 'snm3C_MGC', 'snm3C_MGE-PvSst', 'snm3C_NonN', 'snm3C_ODC',
           'snm3C_OPC', 'snmC_ASC', 'snmC_CA1', 'snmC_CA23', 'snmC_CGE-VipLamp5',
           'snmC_DG', 'snmC_MGC', 'snmC_MGE-PvSst', 'snmC_NonN', 'snmC_ODC',
           'snmC_OPC'], dtype='<U18')

  • sample_collapsed
    (sample_collapsed)
    object
    'ASC' 'CA1' 'CA23' ... 'ODC' 'OPC'

    array(['ASC', 'CA1', 'CA23', 'CGE-VipLamp5', 'DG', 'MGC', 'MGE-PvSst', 'NonN',
           'ODC', 'OPC'], dtype=object)

• Data variables: (4)
  • dmr_da
    (sample, dmr, count_type)
    uint32
    ...

    array([[[4294967295, 4294967295],
            [4294967295, 4294967295],
            ...,
            [4294967295, 4294967295],
            [4294967295, 4294967295]],
    
           [[4294967295, 4294967295],
            [4294967295, 4294967295],
            ...,
            [4294967295, 4294967295],
            [4294967295, 4294967295]],
    
           ...,
    
           [[4294967295, 4294967295],
            [4294967295, 4294967295],
            ...,
            [4294967295, 4294967295],
            [4294967295, 4294967295]],
    
           [[4294967295, 4294967295],
            [4294967295, 4294967295],
            ...,
            [4294967295, 4294967295],
            [4294967295, 4294967295]]], dtype=uint32)

  • dmr_da_frac
    (sample, dmr)
    float32
    ...

    array([[1., 1., 1., ..., 1., 1., 1.],
           [1., 1., 1., ..., 1., 1., 1.],
           [1., 1., 1., ..., 1., 1., 1.],
           ...,
           [1., 1., 1., ..., 1., 1., 1.],
           [1., 1., 1., ..., 1., 1., 1.],
           [1., 1., 1., ..., 1., 1., 1.]], dtype=float32)

  • dmr_state
    (sample, dmr)
    int8
    ...

    array([[-1,  0,  0, ...,  0,  0,  0],
           [ 0,  1,  0, ...,  0, -1,  0],
           [ 0,  1,  0, ..., -1, -1,  0],
           ...,
           [ 0,  0, -1, ...,  0,  0,  0],
           [ 1,  0,  0, ...,  0,  1,  0],
           [ 0,  0, -1, ...,  0,  0,  0]], dtype=int8)

  • dmr_state_collapsed
    (dmr, sample_collapsed)
    int8
    ...

    array([[ 0,  0,  0, ...,  0,  0,  0],
           [ 0,  1,  1, ...,  0,  0,  0],
           [ 0,  0,  0, ..., -1,  0, -1],
           ...,
           [ 0,  0, -1, ...,  0,  0,  0],
           [ 0, -1, -1, ...,  0,  1,  0],
           [ 0,  0,  0, ...,  0,  0,  0]], dtype=int8)

• Attributes: (3)

  chrom_size_path :

  /home/hanliu/pkg/ALLCools_pycharm/docs/allcools/cluster_level/RegionDS/test_HIP/chrom_sizes.txt

  region_dim :

  dmr

  region_ds_location :

  /home/hanliu/pkg/ALLCools_pycharm/docs/allcools/cluster_level/RegionDS/test_HIP

Default Motif Database

The scan_motifs method of RegionDS will perform motif scan using the default motif set over all the regions. This is a time consumming step, scanning 2M regions with 40 CPUs take ~3 days.

dmr_ds.scan_motifs(genome_fasta='../../data/genome/mm10.fa',
                   cpu=45,
                   standardize_length=500,
                   motif_set_path=None,
                   chrom_size_path=None,
                   combine_cluster=True,
                   chunk_size=10000,
                   dim='motif')

index file ../../data/genome/mm10.fa.fai not found, generating...

Scan 2179 motif in 132 sequences.
Job 0 returned

Motif Values

After motif scaning, three value for each motif in each region is stored:

• n_motifs

• max_score

• total_score

dmr_ds.get_index('motif_value')

Index(['n_motifs', 'max_score', 'total_score'], dtype='object', name='motif_value')

Individual motifs

dmr_ds['dmr_motif_da']

<xarray.DataArray 'dmr_motif_da' (dmr: 132, motif: 2179, motif_value: 3)>
array([[[0, 0, 0],
        [0, 0, 0],
        [0, 0, 0],
        ...,
        [0, 0, 0],
        [0, 0, 0],
        [0, 0, 0]],

       [[0, 0, 0],
        [0, 0, 0],
        [0, 0, 0],
        ...,
        [0, 0, 0],
        [0, 0, 0],
        [0, 0, 0]],

       [[0, 0, 0],
        [0, 0, 0],
        [0, 0, 0],
        ...,
...
        ...,
        [0, 0, 0],
        [0, 0, 0],
        [0, 0, 0]],

       [[0, 0, 0],
        [0, 0, 0],
        [0, 0, 0],
        ...,
        [0, 0, 0],
        [0, 0, 0],
        [0, 0, 0]],

       [[0, 0, 0],
        [0, 0, 0],
        [0, 0, 0],
        ...,
        [0, 0, 0],
        [0, 0, 0],
        [0, 0, 0]]], dtype=uint16)
Coordinates:
  * dmr          (dmr) <U9 'chr1-0' 'chr1-1' ... 'chr19-122' 'chr19-123'
    dmr_chrom    (dmr) <U5 'chr1' 'chr1' 'chr1' ... 'chr19' 'chr19' 'chr19'
    dmr_end      (dmr) int64 10002172 10003542 10003967 ... 5099203 5099952
    dmr_length   (dmr) int64 2 305 54 2 2 2 2 ... 589 924 632 842 195 399 335
    dmr_ndms     (dmr) int64 1 7 2 1 1 1 1 13 3 2 1 ... 2 1 2 7 13 19 9 9 3 6 13
    dmr_start    (dmr) int64 10002170 10003237 10003913 ... 5098804 5099617
  * motif        (motif) <U29 'ALX3_homeodomain_2' ... 'ZSC31_HUMAN.H11MO.0.C'
  * motif_value  (motif_value) <U11 'n_motifs' 'max_score' 'total_score'

xarray.DataArray

'dmr_motif_da'

• dmr: 132
• motif: 2179
• motif_value: 3

• 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ... 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0

  array([[[0, 0, 0],
          [0, 0, 0],
          [0, 0, 0],
          ...,
          [0, 0, 0],
          [0, 0, 0],
          [0, 0, 0]],
  
         [[0, 0, 0],
          [0, 0, 0],
          [0, 0, 0],
          ...,
          [0, 0, 0],
          [0, 0, 0],
          [0, 0, 0]],
  
         [[0, 0, 0],
          [0, 0, 0],
          [0, 0, 0],
          ...,
  ...
          ...,
          [0, 0, 0],
          [0, 0, 0],
          [0, 0, 0]],
  
         [[0, 0, 0],
          [0, 0, 0],
          [0, 0, 0],
          ...,
          [0, 0, 0],
          [0, 0, 0],
          [0, 0, 0]],
  
         [[0, 0, 0],
          [0, 0, 0],
          [0, 0, 0],
          ...,
          [0, 0, 0],
          [0, 0, 0],
          [0, 0, 0]]], dtype=uint16)

• Coordinates: (8)
  • dmr
    (dmr)
    <U9
    'chr1-0' 'chr1-1' ... 'chr19-123'

    array(['chr1-0', 'chr1-1', 'chr1-2', 'chr1-3', 'chr1-4', 'chr1-5', 'chr1-6',
           'chr1-7', 'chr19-0', 'chr19-1', 'chr19-2', 'chr19-3', 'chr19-4',
           'chr19-5', 'chr19-6', 'chr19-7', 'chr19-8', 'chr19-9', 'chr19-10',
           'chr19-11', 'chr19-12', 'chr19-13', 'chr19-14', 'chr19-15', 'chr19-16',
           'chr19-17', 'chr19-18', 'chr19-19', 'chr19-20', 'chr19-21', 'chr19-22',
           'chr19-23', 'chr19-24', 'chr19-25', 'chr19-26', 'chr19-27', 'chr19-28',
           'chr19-29', 'chr19-30', 'chr19-31', 'chr19-32', 'chr19-33', 'chr19-34',
           'chr19-35', 'chr19-36', 'chr19-37', 'chr19-38', 'chr19-39', 'chr19-40',
           'chr19-41', 'chr19-42', 'chr19-43', 'chr19-44', 'chr19-45', 'chr19-46',
           'chr19-47', 'chr19-48', 'chr19-49', 'chr19-50', 'chr19-51', 'chr19-52',
           'chr19-53', 'chr19-54', 'chr19-55', 'chr19-56', 'chr19-57', 'chr19-58',
           'chr19-59', 'chr19-60', 'chr19-61', 'chr19-62', 'chr19-63', 'chr19-64',
           'chr19-65', 'chr19-66', 'chr19-67', 'chr19-68', 'chr19-69', 'chr19-70',
           'chr19-71', 'chr19-72', 'chr19-73', 'chr19-74', 'chr19-75', 'chr19-76',
           'chr19-77', 'chr19-78', 'chr19-79', 'chr19-80', 'chr19-81', 'chr19-82',
           'chr19-83', 'chr19-84', 'chr19-85', 'chr19-86', 'chr19-87', 'chr19-88',
           'chr19-89', 'chr19-90', 'chr19-91', 'chr19-92', 'chr19-93', 'chr19-94',
           'chr19-95', 'chr19-96', 'chr19-97', 'chr19-98', 'chr19-99', 'chr19-100',
           'chr19-101', 'chr19-102', 'chr19-103', 'chr19-104', 'chr19-105',
           'chr19-106', 'chr19-107', 'chr19-108', 'chr19-109', 'chr19-110',
           'chr19-111', 'chr19-112', 'chr19-113', 'chr19-114', 'chr19-115',
           'chr19-116', 'chr19-117', 'chr19-118', 'chr19-119', 'chr19-120',
           'chr19-121', 'chr19-122', 'chr19-123'], dtype='<U9')

  • dmr_chrom
    (dmr)
    <U5
    'chr1' 'chr1' ... 'chr19' 'chr19'

    array(['chr1', 'chr1', 'chr1', 'chr1', 'chr1', 'chr1', 'chr1', 'chr1',
           'chr19', 'chr19', 'chr19', 'chr19', 'chr19', 'chr19', 'chr19',
           'chr19', 'chr19', 'chr19', 'chr19', 'chr19', 'chr19', 'chr19',
           'chr19', 'chr19', 'chr19', 'chr19', 'chr19', 'chr19', 'chr19',
           'chr19', 'chr19', 'chr19', 'chr19', 'chr19', 'chr19', 'chr19',
           'chr19', 'chr19', 'chr19', 'chr19', 'chr19', 'chr19', 'chr19',
           'chr19', 'chr19', 'chr19', 'chr19', 'chr19', 'chr19', 'chr19',
           'chr19', 'chr19', 'chr19', 'chr19', 'chr19', 'chr19', 'chr19',
           'chr19', 'chr19', 'chr19', 'chr19', 'chr19', 'chr19', 'chr19',
           'chr19', 'chr19', 'chr19', 'chr19', 'chr19', 'chr19', 'chr19',
           'chr19', 'chr19', 'chr19', 'chr19', 'chr19', 'chr19', 'chr19',
           'chr19', 'chr19', 'chr19', 'chr19', 'chr19', 'chr19', 'chr19',
           'chr19', 'chr19', 'chr19', 'chr19', 'chr19', 'chr19', 'chr19',
           'chr19', 'chr19', 'chr19', 'chr19', 'chr19', 'chr19', 'chr19',
           'chr19', 'chr19', 'chr19', 'chr19', 'chr19', 'chr19', 'chr19',
           'chr19', 'chr19', 'chr19', 'chr19', 'chr19', 'chr19', 'chr19',
           'chr19', 'chr19', 'chr19', 'chr19', 'chr19', 'chr19', 'chr19',
           'chr19', 'chr19', 'chr19', 'chr19', 'chr19', 'chr19', 'chr19',
           'chr19', 'chr19', 'chr19', 'chr19', 'chr19'], dtype='<U5')

  • dmr_end
    (dmr)
    int64
    10002172 10003542 ... 5099952

    array([10002172, 10003542, 10003967, 10005479, 10007099, 10007758,
           10008881, 10009927,  5000194,  5000343,  5000715,  5001506,
            5001549,  5003862,  5004785,  5005319,  5005816,  5006789,
            5008015,  5008084,  5008130,  5008805,  5010091,  5011268,
            5011724,  5011926,  5012429,  5012955,  5013312,  5013603,
            5014250,  5014562,  5014921,  5015099,  5016145,  5016791,
            5017181,  5017656,  5018165,  5018340,  5019014,  5019656,
            5020498,  5021894,  5022034,  5022299,  5023452,  5025645,
            5026013,  5026581,  5028070,  5029223,  5029469,  5029930,
            5031623,  5032343,  5033665,  5035273,  5036180,  5036656,
            5037800,  5040294,  5040872,  5042216,  5042541,  5043207,
            5043818,  5045206,  5046083,  5046469,  5047139,  5050164,
            5051764,  5054110,  5055419,  5056089,  5056189,  5056309,
            5056642,  5057152,  5057233,  5059280,  5059541,  5060286,
            5060636,  5061033,  5061586,  5062181,  5062652,  5063270,
            5064727,  5065461,  5065765,  5066074,  5066405,  5067916,
            5069149,  5070132,  5071656,  5071800,  5073983,  5074921,
            5076037,  5076379,  5077207,  5078490,  5078805,  5080040,
            5080229,  5081032,  5081240,  5081796,  5082893,  5083285,
            5083313,  5083586,  5084274,  5084686,  5086323,  5087101,
            5087539,  5089466,  5089734,  5090283,  5091820,  5092737,
            5094022,  5095601,  5097380,  5097870,  5099203,  5099952])

  • dmr_length
    (dmr)
    int64
    2 305 54 2 2 ... 842 195 399 335

    array([   2,  305,   54,    2,    2,    2,    2,  440,  171,   12,    2,
              2,   22,  504,  128,  146,  201,    2,    2,    2,    2,  182,
              2,  246,    2,    2,  101,  343,   49,  183,    2,   88,    2,
              2,   89,  385,   55,    2,    2,   48,  144,    2,    2,  821,
              2,    2,  306,  913,    2,   71,   91,   22,   21,  149,    2,
              2,    2,    2,   57,   76,    2,  532,  552,  211,    2,  243,
              2,    2,  322,   63,    2, 2314, 1029, 2090,    2,   58,    2,
             67,    2,  253,    2, 1351,    2,  478,    2,  127,   42,   43,
              2,   46,    2,  482,   14,    2,    2,  773,  760,    2,  661,
            126,  345,  687,  537,    2,  469,  866,    2,    2,   59,  315,
              2,  368, 1053,  367,    2,    2,  186,    2,  391,  108,  323,
             31,    2,  138,  434,  589,  924,  632,  842,  195,  399,  335])

  • dmr_ndms
    (dmr)
    int64
    1 7 2 1 1 1 1 ... 13 19 9 9 3 6 13

    array([ 1,  7,  2,  1,  1,  1,  1, 13,  3,  2,  1,  1,  2,  5,  2,  3,  2,
            1,  1,  1,  1,  4,  1,  2,  1,  1,  3,  6,  4,  3,  1,  4,  1,  1,
            3,  7,  4,  1,  1,  2,  4,  1,  1,  8,  1,  1,  9, 14,  1,  5,  3,
            2,  2,  2,  1,  1,  1,  1,  2,  2,  1, 17, 11,  3,  1,  5,  1,  1,
            9,  4,  1, 33, 28, 56,  1,  2,  1,  2,  1,  4,  1, 20,  1,  7,  1,
            2,  2,  2,  1,  2,  1,  7,  3,  1,  1, 15, 29,  1, 20,  4,  8, 13,
            4,  1,  5, 15,  1,  1,  4,  6,  1, 10, 47,  9,  1,  1,  2,  1,  3,
            4,  8,  2,  1,  2,  7, 13, 19,  9,  9,  3,  6, 13])

  • dmr_start
    (dmr)
    int64
    10002170 10003237 ... 5099617

    array([10002170, 10003237, 10003913, 10005477, 10007097, 10007756,
           10008879, 10009487,  5000023,  5000331,  5000713,  5001504,
            5001527,  5003358,  5004657,  5005173,  5005615,  5006787,
            5008013,  5008082,  5008128,  5008623,  5010089,  5011022,
            5011722,  5011924,  5012328,  5012612,  5013263,  5013420,
            5014248,  5014474,  5014919,  5015097,  5016056,  5016406,
            5017126,  5017654,  5018163,  5018292,  5018870,  5019654,
            5020496,  5021073,  5022032,  5022297,  5023146,  5024732,
            5026011,  5026510,  5027979,  5029201,  5029448,  5029781,
            5031621,  5032341,  5033663,  5035271,  5036123,  5036580,
            5037798,  5039762,  5040320,  5042005,  5042539,  5042964,
            5043816,  5045204,  5045761,  5046406,  5047137,  5047850,
            5050735,  5052020,  5055417,  5056031,  5056187,  5056242,
            5056640,  5056899,  5057231,  5057929,  5059539,  5059808,
            5060634,  5060906,  5061544,  5062138,  5062650,  5063224,
            5064725,  5064979,  5065751,  5066072,  5066403,  5067143,
            5068389,  5070130,  5070995,  5071674,  5073638,  5074234,
            5075500,  5076377,  5076738,  5077624,  5078803,  5080038,
            5080170,  5080717,  5081238,  5081428,  5081840,  5082918,
            5083311,  5083584,  5084088,  5084684,  5085932,  5086993,
            5087216,  5089435,  5089732,  5090145,  5091386,  5092148,
            5093098,  5094969,  5096538,  5097675,  5098804,  5099617])

  • motif
    (motif)
    <U29
    'ALX3_homeodomain_2' ... 'ZSC31_...

    array(['ALX3_homeodomain_2', 'ALX3_homeodomain_3', 'ALX4_homeodomain_1', ...,
           'ZNF8_HUMAN.H11MO.0.C', 'ZSC22_HUMAN.H11MO.0.C',
           'ZSC31_HUMAN.H11MO.0.C'], dtype='<U29')

  • motif_value
    (motif_value)
    <U11
    'n_motifs' ... 'total_score'

    array(['n_motifs', 'max_score', 'total_score'], dtype='<U11')

• Attributes: (0)

Motif Clusters

dmr_ds['dmr_motif-cluster_da']

<xarray.DataArray 'dmr_motif-cluster_da' (motif-cluster: 286, dmr: 132, motif_value: 3)>
[113256 values with dtype=uint16]
Coordinates:
  * dmr            (dmr) <U9 'chr1-0' 'chr1-1' ... 'chr19-122' 'chr19-123'
    dmr_chrom      (dmr) <U5 'chr1' 'chr1' 'chr1' ... 'chr19' 'chr19' 'chr19'
    dmr_end        (dmr) int64 10002172 10003542 10003967 ... 5099203 5099952
    dmr_length     (dmr) int64 2 305 54 2 2 2 2 ... 589 924 632 842 195 399 335
    dmr_ndms       (dmr) int64 1 7 2 1 1 1 1 13 3 2 1 ... 1 2 7 13 19 9 9 3 6 13
    dmr_start      (dmr) int64 10002170 10003237 10003913 ... 5098804 5099617
  * motif_value    (motif_value) <U11 'n_motifs' 'max_score' 'total_score'
  * motif-cluster  (motif-cluster) object 'c1' 'c10' 'c100' ... 'c98' 'c99'

xarray.DataArray

'dmr_motif-cluster_da'

• motif-cluster: 286
• dmr: 132
• motif_value: 3

• ...

  [113256 values with dtype=uint16]

• Coordinates: (8)
  • dmr
    (dmr)
    <U9
    'chr1-0' 'chr1-1' ... 'chr19-123'

    array(['chr1-0', 'chr1-1', 'chr1-2', 'chr1-3', 'chr1-4', 'chr1-5', 'chr1-6',
           'chr1-7', 'chr19-0', 'chr19-1', 'chr19-2', 'chr19-3', 'chr19-4',
           'chr19-5', 'chr19-6', 'chr19-7', 'chr19-8', 'chr19-9', 'chr19-10',
           'chr19-11', 'chr19-12', 'chr19-13', 'chr19-14', 'chr19-15', 'chr19-16',
           'chr19-17', 'chr19-18', 'chr19-19', 'chr19-20', 'chr19-21', 'chr19-22',
           'chr19-23', 'chr19-24', 'chr19-25', 'chr19-26', 'chr19-27', 'chr19-28',
           'chr19-29', 'chr19-30', 'chr19-31', 'chr19-32', 'chr19-33', 'chr19-34',
           'chr19-35', 'chr19-36', 'chr19-37', 'chr19-38', 'chr19-39', 'chr19-40',
           'chr19-41', 'chr19-42', 'chr19-43', 'chr19-44', 'chr19-45', 'chr19-46',
           'chr19-47', 'chr19-48', 'chr19-49', 'chr19-50', 'chr19-51', 'chr19-52',
           'chr19-53', 'chr19-54', 'chr19-55', 'chr19-56', 'chr19-57', 'chr19-58',
           'chr19-59', 'chr19-60', 'chr19-61', 'chr19-62', 'chr19-63', 'chr19-64',
           'chr19-65', 'chr19-66', 'chr19-67', 'chr19-68', 'chr19-69', 'chr19-70',
           'chr19-71', 'chr19-72', 'chr19-73', 'chr19-74', 'chr19-75', 'chr19-76',
           'chr19-77', 'chr19-78', 'chr19-79', 'chr19-80', 'chr19-81', 'chr19-82',
           'chr19-83', 'chr19-84', 'chr19-85', 'chr19-86', 'chr19-87', 'chr19-88',
           'chr19-89', 'chr19-90', 'chr19-91', 'chr19-92', 'chr19-93', 'chr19-94',
           'chr19-95', 'chr19-96', 'chr19-97', 'chr19-98', 'chr19-99', 'chr19-100',
           'chr19-101', 'chr19-102', 'chr19-103', 'chr19-104', 'chr19-105',
           'chr19-106', 'chr19-107', 'chr19-108', 'chr19-109', 'chr19-110',
           'chr19-111', 'chr19-112', 'chr19-113', 'chr19-114', 'chr19-115',
           'chr19-116', 'chr19-117', 'chr19-118', 'chr19-119', 'chr19-120',
           'chr19-121', 'chr19-122', 'chr19-123'], dtype='<U9')

  • dmr_chrom
    (dmr)
    <U5
    'chr1' 'chr1' ... 'chr19' 'chr19'

    array(['chr1', 'chr1', 'chr1', 'chr1', 'chr1', 'chr1', 'chr1', 'chr1',
           'chr19', 'chr19', 'chr19', 'chr19', 'chr19', 'chr19', 'chr19',
           'chr19', 'chr19', 'chr19', 'chr19', 'chr19', 'chr19', 'chr19',
           'chr19', 'chr19', 'chr19', 'chr19', 'chr19', 'chr19', 'chr19',
           'chr19', 'chr19', 'chr19', 'chr19', 'chr19', 'chr19', 'chr19',
           'chr19', 'chr19', 'chr19', 'chr19', 'chr19', 'chr19', 'chr19',
           'chr19', 'chr19', 'chr19', 'chr19', 'chr19', 'chr19', 'chr19',
           'chr19', 'chr19', 'chr19', 'chr19', 'chr19', 'chr19', 'chr19',
           'chr19', 'chr19', 'chr19', 'chr19', 'chr19', 'chr19', 'chr19',
           'chr19', 'chr19', 'chr19', 'chr19', 'chr19', 'chr19', 'chr19',
           'chr19', 'chr19', 'chr19', 'chr19', 'chr19', 'chr19', 'chr19',
           'chr19', 'chr19', 'chr19', 'chr19', 'chr19', 'chr19', 'chr19',
           'chr19', 'chr19', 'chr19', 'chr19', 'chr19', 'chr19', 'chr19',
           'chr19', 'chr19', 'chr19', 'chr19', 'chr19', 'chr19', 'chr19',
           'chr19', 'chr19', 'chr19', 'chr19', 'chr19', 'chr19', 'chr19',
           'chr19', 'chr19', 'chr19', 'chr19', 'chr19', 'chr19', 'chr19',
           'chr19', 'chr19', 'chr19', 'chr19', 'chr19', 'chr19', 'chr19',
           'chr19', 'chr19', 'chr19', 'chr19', 'chr19', 'chr19', 'chr19',
           'chr19', 'chr19', 'chr19', 'chr19', 'chr19'], dtype='<U5')

  • dmr_end
    (dmr)
    int64
    10002172 10003542 ... 5099952

    array([10002172, 10003542, 10003967, 10005479, 10007099, 10007758,
           10008881, 10009927,  5000194,  5000343,  5000715,  5001506,
            5001549,  5003862,  5004785,  5005319,  5005816,  5006789,
            5008015,  5008084,  5008130,  5008805,  5010091,  5011268,
            5011724,  5011926,  5012429,  5012955,  5013312,  5013603,
            5014250,  5014562,  5014921,  5015099,  5016145,  5016791,
            5017181,  5017656,  5018165,  5018340,  5019014,  5019656,
            5020498,  5021894,  5022034,  5022299,  5023452,  5025645,
            5026013,  5026581,  5028070,  5029223,  5029469,  5029930,
            5031623,  5032343,  5033665,  5035273,  5036180,  5036656,
            5037800,  5040294,  5040872,  5042216,  5042541,  5043207,
            5043818,  5045206,  5046083,  5046469,  5047139,  5050164,
            5051764,  5054110,  5055419,  5056089,  5056189,  5056309,
            5056642,  5057152,  5057233,  5059280,  5059541,  5060286,
            5060636,  5061033,  5061586,  5062181,  5062652,  5063270,
            5064727,  5065461,  5065765,  5066074,  5066405,  5067916,
            5069149,  5070132,  5071656,  5071800,  5073983,  5074921,
            5076037,  5076379,  5077207,  5078490,  5078805,  5080040,
            5080229,  5081032,  5081240,  5081796,  5082893,  5083285,
            5083313,  5083586,  5084274,  5084686,  5086323,  5087101,
            5087539,  5089466,  5089734,  5090283,  5091820,  5092737,
            5094022,  5095601,  5097380,  5097870,  5099203,  5099952])

  • dmr_length
    (dmr)
    int64
    2 305 54 2 2 ... 842 195 399 335

    array([   2,  305,   54,    2,    2,    2,    2,  440,  171,   12,    2,
              2,   22,  504,  128,  146,  201,    2,    2,    2,    2,  182,
              2,  246,    2,    2,  101,  343,   49,  183,    2,   88,    2,
              2,   89,  385,   55,    2,    2,   48,  144,    2,    2,  821,
              2,    2,  306,  913,    2,   71,   91,   22,   21,  149,    2,
              2,    2,    2,   57,   76,    2,  532,  552,  211,    2,  243,
              2,    2,  322,   63,    2, 2314, 1029, 2090,    2,   58,    2,
             67,    2,  253,    2, 1351,    2,  478,    2,  127,   42,   43,
              2,   46,    2,  482,   14,    2,    2,  773,  760,    2,  661,
            126,  345,  687,  537,    2,  469,  866,    2,    2,   59,  315,
              2,  368, 1053,  367,    2,    2,  186,    2,  391,  108,  323,
             31,    2,  138,  434,  589,  924,  632,  842,  195,  399,  335])

  • dmr_ndms
    (dmr)
    int64
    1 7 2 1 1 1 1 ... 13 19 9 9 3 6 13

    array([ 1,  7,  2,  1,  1,  1,  1, 13,  3,  2,  1,  1,  2,  5,  2,  3,  2,
            1,  1,  1,  1,  4,  1,  2,  1,  1,  3,  6,  4,  3,  1,  4,  1,  1,
            3,  7,  4,  1,  1,  2,  4,  1,  1,  8,  1,  1,  9, 14,  1,  5,  3,
            2,  2,  2,  1,  1,  1,  1,  2,  2,  1, 17, 11,  3,  1,  5,  1,  1,
            9,  4,  1, 33, 28, 56,  1,  2,  1,  2,  1,  4,  1, 20,  1,  7,  1,
            2,  2,  2,  1,  2,  1,  7,  3,  1,  1, 15, 29,  1, 20,  4,  8, 13,
            4,  1,  5, 15,  1,  1,  4,  6,  1, 10, 47,  9,  1,  1,  2,  1,  3,
            4,  8,  2,  1,  2,  7, 13, 19,  9,  9,  3,  6, 13])

  • dmr_start
    (dmr)
    int64
    10002170 10003237 ... 5099617

    array([10002170, 10003237, 10003913, 10005477, 10007097, 10007756,
           10008879, 10009487,  5000023,  5000331,  5000713,  5001504,
            5001527,  5003358,  5004657,  5005173,  5005615,  5006787,
            5008013,  5008082,  5008128,  5008623,  5010089,  5011022,
            5011722,  5011924,  5012328,  5012612,  5013263,  5013420,
            5014248,  5014474,  5014919,  5015097,  5016056,  5016406,
            5017126,  5017654,  5018163,  5018292,  5018870,  5019654,
            5020496,  5021073,  5022032,  5022297,  5023146,  5024732,
            5026011,  5026510,  5027979,  5029201,  5029448,  5029781,
            5031621,  5032341,  5033663,  5035271,  5036123,  5036580,
            5037798,  5039762,  5040320,  5042005,  5042539,  5042964,
            5043816,  5045204,  5045761,  5046406,  5047137,  5047850,
            5050735,  5052020,  5055417,  5056031,  5056187,  5056242,
            5056640,  5056899,  5057231,  5057929,  5059539,  5059808,
            5060634,  5060906,  5061544,  5062138,  5062650,  5063224,
            5064725,  5064979,  5065751,  5066072,  5066403,  5067143,
            5068389,  5070130,  5070995,  5071674,  5073638,  5074234,
            5075500,  5076377,  5076738,  5077624,  5078803,  5080038,
            5080170,  5080717,  5081238,  5081428,  5081840,  5082918,
            5083311,  5083584,  5084088,  5084684,  5085932,  5086993,
            5087216,  5089435,  5089732,  5090145,  5091386,  5092148,
            5093098,  5094969,  5096538,  5097675,  5098804,  5099617])

  • motif_value
    (motif_value)
    <U11
    'n_motifs' ... 'total_score'

    array(['n_motifs', 'max_score', 'total_score'], dtype='<U11')

  • motif-cluster
    (motif-cluster)
    object
    'c1' 'c10' 'c100' ... 'c98' 'c99'

    array(['c1', 'c10', 'c100', ..., 'c97', 'c98', 'c99'], dtype=object)

• Attributes: (0)

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