Gene frequencies tab

This tab gives information on the frequency of V, D and J gene usage.

Graphs

Distribution of V gene families

Bar graph showing the frequency of V gene family usage in all uploaded donors.

Relative frequency of V gene usage

Bar graph showing the frequency of V genes in all uploaded donors. The order of the V genes on the x-axis can be altered by altering the “Order of V(D)J genes in graphs” filter on the main page of the Immune repertoire pipeline.

Relative frequency of D gene usage

Bar graph showing the frequency of D genes in all uploaded donors. The order of the D genes on the x-axis can be altered by altering the “Order of V(D)J genes in graphs” filter on the main page of the Immune repertoire pipeline.

Relative frequency of J gene usage

Bar graph showing the frequency of J genes in all uploaded donors. The order of the J genes on the x-axis can be altered by altering the “Order of V(D)J genes in graphs” filter on the main page of the Immune repertoire pipeline.

D reading frame

Bar graph visualizing the frequency by which each D reading frame is used in each donor.

Donor | Median CDR3 Length
--- | ---
ID_WITH_SPACES | 13

CDR3 characteristics tab

This tab gives information on the different characteristics of the CDR3.

Graphs

length distribution of CDR3

Graph visualizing for each donor the distribution of the CDR3 length in amino acids between all sequences.

Amino acid composition of CDR3

Bar graph visualizing for each donor how frequent each amino acid is used in the CDR3 of all sequences. The red colour in the background indicate positively charged amino acids, and the blue colour in the background indicate negatively charged amino acids. The amino acids are ordered from hydrophilic (left) to hydrophobic (right).

Table

Table showing for each donor the median CDR3 length.

In this tab heatmaps are provided showing the frequency of different combinations V and D, D and J and V and J genes according together. For each donor a subtab with all three heatmaps is provided.

ID | Include
--- | ---
ID_WITH_SPACES |

The tab allows you to compare the VD, VJ and DJ heatmaps of multiple donors to each other.

By ticking the include box of a donor, the three heatmaps of this donor is visualized underneath eachother. By clicking the include box of multiple replicates the heatmaps of these replicates are visualized next to each other allowing easy comparison of heatmaps.

V-J |

Martin Krzywinski, Jacqueline Schein, İnanç Birol, Joseph Connors, Randy Gascoyne, Doug Horsman, Steven J. Jones and Marco A. Marra (2009). Circos: An information aesthetic for comparative genomics. In Genome Research 10.1101/gr.092759.109.

Circos plot showing the V-D, V-J, and D-J gen usage. The thicker the line the more frequent this gene combination is used.

Unique rearrangements with a V, D and J gene assigned

Productive mean
Donor | Number of sequences | V.DEL | P1 | N1 | P2 | DEL.D | D.DEL | P3 | N2 | P4 | DEL.J | Total.Del | Total.N | Total.P | CDR3.Length
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ID_WITH_SPACES | 11049 | 1.5 | 0.2 | 5.3 | 0.1 | 7.2 | 5.5 | 0.1 | 5.6 | 0.1 | 6.8 | 21 | 10.9 | 0.4 | 13

Unproductive mean
Donor | Number of sequences | V.DEL | P1 | N1 | P2 | DEL.D | D.DEL | P3 | N2 | P4 | DEL.J | Total.Del | Total.N | Total.P | CDR3.Length
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ID_WITH_SPACES | 2705 | 2 | 0.2 | 7.8 | 0.1 | 7.1 | 4.5 | 0 | 10 | 0 | 12.1 | 25.7 | 17.8 | 0.4 | -

Productive median
Donor | Number of sequences | V.DEL | P1 | N1 | P2 | DEL.D | D.DEL | P3 | N2 | P4 | DEL.J | Total.Del | Total.N | Total.P | CDR3.Length
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ID_WITH_SPACES | 11049 | 1 | 0 | 4 | 0 | 6 | 4 | 0 | 5 | 0 | 6 | 21 | 10 | 0 | 13

Unproductive median
Donor | Number of sequences | V.DEL | P1 | N1 | P2 | DEL.D | D.DEL | P3 | N2 | P4 | DEL.J | Total.Del | Total.N | Total.P | CDR3.Length
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ID_WITH_SPACES | 2705 | 1 | 0 | 6 | 0 | 6 | 3 | 0 | 10 | 0 | 15 | 26 | 17 | 0 | -

Unique rearrangements with only a V and J gene assigned

Productive mean
Donor | Number of sequences | V.DEL | P1 | N | P2 | DEL.J | Total.Del | Total.N | Total.P | CDR3.Length
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ID_WITH_SPACES | 98 | 1.1 | 0.3 | 3.2 | 0 | 4.7 | 1.1 | 3.2 | 0.1 | 8

Unproductive mean
Donor | Number of sequences | V.DEL | P1 | N | P2 | DEL.J | Total.Del | Total.N | Total.P | CDR3.Length
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ID_WITH_SPACES | 89 | 1 | 0 | 3 | 0 | 0 | 0 | 3 | 0 | -

Productive median
Donor | Number of sequences | V.DEL | P1 | N | P2 | DEL.J | Total.Del | Total.N | Total.P | CDR3.Length
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ID_WITH_SPACES | 98 | 1 | 0 | 3 | 0 | 2.5 | 0 | 3 | 0 | 8

Unproductive median
Donor | Number of sequences | V.DEL | P1 | N | P2 | DEL.J | Total.Del | Total.N | Total.P | CDR3.Length
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ID_WITH_SPACES | 89 | 1 | 0 | 3 | 0 | 0 | 0 | 3 | 0 | -

Junction analysis tab

Tables:

The unique rearrangements are separated in sequences that contain both a V, D and J gene and sequences that contain only a V and J gene.

Productive mean tables

Reports for each donor the number of productive sequences and the mean number of deletions, N-nucleotides and P-nucleotides. For explanation about the different deletions and N and P nucleotides see figure above.

Unproductive mean table

Reports for each donor the number of unproductive sequences and the mean number of deletions, N-nucleotides and P-nucleotides. For explanation about the different deletions and N and P nucleotides see figure above.

Productive median table

Reports for each donor the number of productive sequences and the median number of deletions, N-nucleotides and P-nucleotides. For explanation about the different deletions and N and P nucleotides see figure above.

Unproductive median table

Reports for each donor the number of unproductive sequences and the median number of deletions, N-nucleotides and P-nucleotides. For explanation about the different deletions and N and P nucleotides see figure above.

Description | Link
--- | ---
All outputs below in a zip file | Download
The filtered dataset | Download
Gene frequencies
The dataset used to generate the distribution of V gene families graph | Download
The dataset used to generate the relative frequency of V gene usage graph | Download
The dataset used to generate the relative frequency of J gene usage graph | Download
The dataset used to generate the relative frequency of the D reading frame graph | Download
CDR3 Characteristics
The dataset used to generate the CDR3 length frequency graph | Download
The dataset used to generate the Amino Acid Composition in the CDR3 graph | Download
Heatmaps
The data used to generate the VJ heatmap for ID_WITH_SPACES. | Download
Circos
The data used to generate the VJ Circos plots for ID_WITH_SPACES. | Download
Clonality
The dataset used to calculate clonality score (Unique based on clonaltype, none) | Download

Downloads tab

Description

The filtered dataset: Allows you to download information on V D and J gene usage, the junctions and the amino acid sequence of the sequences that passed the chosen filter settings. Note: this file contains only 1 sequences of a replicate sequence.

Gene frequencies

The dataset used to generate the distribution of V gene families graph: Downloads a table with information used to generate the distribution of V gene families graph.

The dataset used to generate the distribution of D gene families graph: Downloads a table with information used to generate the distribution of D gene families graph.

The dataset used to generate the relative frequency of V gene usage graph: Downloads the data used to generate the relative frequency of V gene usage graph. In addition information on the chromosomal order of the V genes can be found.

The dataset used to generate the relative frequency of D gene usage graph: Downloads the data used to generate the relative frequency of D gene usage graph. In addition information on the chromosomal order of the D genes can be found.

The dataset used to generate the relative frequency of J gene usage graph: Downloads the data used to generate the relative frequency of J gene usage graph. In addition information on the chromosomal order of the J genes can be found.

The dataset used to generate the relative frequency of the D reading frame graph: Downloads the data used to generate the relative frequency of the D reading frame.

CDR3 characteristics

The dataset used to generate the CDR3 length frequency graph: Downloads a table with information used for the length distribution of CDR3 plot.

The dataset used to generate the Amino Acid Composition in the CDR3 graph: Downloads the frequency of the different amino acids in the CDR3 of all filtered sequences. This data set is used for the generation of the Amino Acid Composition in the CDR3 graph. In addition the order of amino acids based on hydrophobicity in included.

Heatmaps

The data used to generate the VD heatmap for “donor name”: Downloads the data set used for the generation of the VD heatmap. For each uploaded donor a separate download is generated.

The data used to generate the VJ heatmap for “donor name”: Downloads the data set used for the generation of the VJ heatmap. For each uploaded donor a separate download is generated.

The data used to generate the DJ heatmap for “sample name”: Downloads the data set used for the generation of the DJ heatmap. For each uploaded donor a separate download is generated.

Circos

The data used to generate the VD circus plots for “donor name”: Downloads the data set used for the generation of the VD heatmap. For each uploaded donor a separate download is generated.

The data used to generate the VJ circus plots for “donor name”: Downloads the data set used for the generation of the VJ heatmap. For each uploaded donor a separate download is generated.

The data used to generate the DJ circus plots for “sample name”: Downloads the data set used for the generation of the DJ heatmap. For each uploaded donor a separate download is generated.

Clonality

The dataset used to calculate clonality score: Allows you to download information on V D and J gene usage, the junctions and the amino acid sequence of the sequences that passed the chosen filter settings. Note: this file contains all the replicate sequences form the different input files.

Sequences that are present in more than one replicate: Allows you to download a table containing all the sequences that were present in more than one replicate. It provides the concidence type, clonaltype, sequence name, replicate number, and the nucleotide sequence