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
| 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 |
| 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 | - |
| 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 |
| 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
| 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 |
| 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 | - |
| 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 |
| 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