HPV VIS-Cistrome Factor Overlap in each human chromosome

This page provides a heatmap of three VIS-Factors overlap counts by chromosome to help users have a better understanding of the distribution of VIS-Factors overlap in the human genome.

HPV Overall Heatmap

CA: chromatin accessibility TFBS: transcription factor binding site HM: histone modification

Browse data distribution by Chromosome or Factor

*Please select the Chromosome or Factor you are interested in, the page will be automatically redirected.

Chromosome:

Cistrome Factor:

VIS locations with VIS-cistrome overlap information and VIS details for each chromosome

Show VIS with one point

Rank of Overlapped Records (S)	DVID	Location	HM (S)	TFBS (S)	CA (S)	Sum (S)	HM (B)	TFBS (B)	CA (B)	Sum (B)	Case/Length	Detail
1	5000768	37540631, 37540738	77	7	3	87	77	8	3	88	Case 1 \| 107	View
2	5001663	22054913, 22054971	25			25	25	1		26	Case 1 \| 58	View
3	5000094	244066950, 244080304	23	1		24	1585	675	777	3037	Case 1 \| 13354	View
4	5000231	171107837, 171117158	3	9	6	18	150	259	302	711	Case 1 \| 9321	View
5	5402940	201287952, 201287970	7	3		10	8	3		11	Case 1 \| 18	View
6	5000052	213965900, 214035795	2			2	3679	2585	1312	7576	Case 1 \| 69895	View
7	5001953	244169110, 244169844	1	1		2	1	15	2	18	Case 1 \| 734	View
8	5000050	213965966, 214025459	2			2	3624	2491	1281	7396	Case 1 \| 59493	View
9	5004238	199471058, 199471113	1			1	1			1	Case 1 \| 55	View
10	5500049	152213926, 152215378				0	318	104	27	449	Case 2 \| 1452	View

View VIS-VM Association

View the association between Viral Integration Sequence (VIS) and Virus Mutation (VM) in HPV

Contents
Description

VIS-Cistrome factor overlapping Description

The overlaps between integration site and cistrome are retrieved by genome search engine GIGGLE (Ryan M Layer et al. 2018). We built three indexs including histone modification, transcription factor binding site and chromatin accessibility, then we searched the significance of shared genomic loci (overlaps) between query VIS and Cistrome (Rongbin Zheng et al. 2019) genome interval files. So one VIS may have several overlaps with multiple Cistrome factor-related samples, the associated factor and overlap amount could indicate that the virus integration site is a potentially functional DNA element.

HPV Overall Heatmap

This heatmap is an overall statistics for HPV VIS-Cistrome factor overlapped records by chromosome. The darker the red, the greater the overlapped records number. The user can view specific number by moving mouse pointer.

Browse data by Chromosome or Factor

The user can browse HPV VIS-Cistrome factor overlapped records data by specific chromosome or statistics histogram for specific Cistrome factor when users click the chromosome or Cistrome factor the user are interested in.

VIS locations with VIS-cistrome overlap information and VIS details for each chromosome

This table showed the VIS locations with VIS-cistrome overlap information and VIS details for each chromosome, you can click green button with number which indicates the overlapped records of this VIS and 3 cistrome factor (histone modification, transcription factor binding site and chromatin accessibility) to inspect details of cistrome sample and factor information, you can click "Detail" button to inspect other information of this VIS.

Case 1
： The deletion of human fragments during the integration event.

Case 2
： Due to the experimental method/design, two viral insertion positions were provided in the literature.
Length:
~40 bp

41 bp~1000 bp

1001 bp~


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