CN111709219B

CN111709219B - Method for personalized display of single omics and multi-group science KEGG PATHWAY map expression heatmaps and application

Info

Publication number: CN111709219B
Application number: CN202010349145.8A
Authority: CN
Inventors: 肖云平; 公光业; 范美婷; 郝瑜琪; 王树伟; 史贤俊; 林博; 刘钰钏
Original assignee: Shanghai Oe Biotech Co ltd
Current assignee: Shanghai Oe Biotech Co ltd
Priority date: 2020-04-28
Filing date: 2020-04-28
Publication date: 2021-06-18
Anticipated expiration: 2040-04-28
Also published as: CN111709219A

Abstract

The invention provides a method for individually displaying single omics and multi-group chemistry KEGG PATHWAY map expression heatmaps and application thereof, wherein in KEGG PATHWAY map combined in multi-omics, the expression, difference level and significance of each omics element in each KEGG PATHWAY map are simultaneously displayed in batch in modes of color scale, element filling color, element graph display and the like. Based on the invention, KEGG PATHWAY map can be expanded in the range of single-component chemistry and multi-component chemistry, can be processed in batch and modified in a personalized way, and can clearly and specifically display the expression and significance of elements in different forms in different scales from single-component chemistry to multi-component science in transcription, protein and metabolism.

Description

Method for personalized display of single omics and multi-group science KEGG PATHWAY map expression heatmaps and application

Technical Field

The invention belongs to the technical field of biological information, and relates to a method for personalized display of a single omics and multi-group science KEGG PATHWAY map expression heat map and application thereof.

Background

The KEGG database was a public database established by Kanehisa laboratories of bioinformatics center of Kyoto university, Japan in 1995 for systematically analyzing gene functions, and it links information of genome with gene functions for the purpose of revealing genetic and chemical blueprints of life phenomena. KEGG PATHWAY is one of the most core databases of KEGG. KEGG PATHWAY database contains the manual hand-drawn path diagram, and shows the intermolecular interaction and the intermolecular interaction network. In transcriptome, proteome and metabolome, the differential gene (transcript), differential protein or differential metabolite mapped to KEGG PATHWAY is often displayed specially in the form of KEGG pathway map, for example, according to the comparison result of transcriptome gene difference, up-regulated gene is displayed in dark green, down-regulated gene is displayed in KEGG map in red, so as to visually understand the role of differential gene in KEGG metabolic pathway. In single-component chemistry, the up-and-down information is expressed by colors such as red, green and blue, and the specific expression values of genes, proteins and metabolites cannot be intuitively understood. In omics associations, such as transcriptome-proteome associations, since genes and transcripts occupy the same positional box, it is not possible to visually display specific fold-of-difference or expression values despite the fact that the box is divided.

Some integrated software, such as pathview and mapman, can realize visual display of expression values by a heat map method, but have more limiting factors, such as species limitation, incapability of setting colors and scales in a personalized manner, limitation to monoomics, and incapability of realizing common display of multiple groups of mathematics. In the case of a multiomic association, especially a transcriptome, proteome and metabolome association, because the expression or differential expression ranges of genes, proteins and metabolites are different, the expression of elements with smaller ranges can be indistinguishable by using the same scale. The existing method and software are not realized in omics combination, each single omics has a separate scale, and personalized adjustment and adaptation can be carried out so as to visually display the specific expression or differential expression level of each element in the kegg map.

Disclosure of Invention

In view of the above technical problems, the present invention aims to provide a method for personalized display of KEGG PATHWAY map expression heatmaps in single-component and multiple-component science and applications thereof, wherein a bioinformatics method is applied to single-component omics of animal and plant bacteria and the like to visually display (differential) expression levels of genes, proteins or metabolites, and applied to multiple-component omics to visually display (differential) expression levels of genes, proteins and metabolites on different heatmap scales.

In order to achieve the technical purpose, the invention adopts the following technical scheme:

according to one aspect of the invention, the invention provides a method for personalized display of a single omics and multi-group science KEGG PATHWAY map expression heatmap, comprising a single omics method and a multi-group science method, wherein the single omics method comprises the following steps:

1) matching the annotation elements to an html file of KEGG PATHWAY according to the expression or differential expression level information of the known target genes, proteins or metabolites and corresponding annotated elements in KEGG PATHWAY to obtain coordinate information of the annotated elements in KEGG PATHWAY map pictures;

2) for each KEGG PATHWAY annotated by the target gene, protein or metabolite, acquiring the integer values of the upper and lower extreme values of expression or differential expression of all genes, proteins or metabolites in KEGG PATHWAY as the upper and lower limits of the color scale of the expression heatmap;

3) dividing the upper limit and the lower limit into a certain equal part to form an arithmetic progression from a minimum value to a maximum value, and giving a color to the scale;

4) matching to a corresponding range interval according to the expression or differential expression value of each gene, protein or metabolite under KEGG PATHWAY to obtain corresponding attribution color;

5) drawing a ruler on KEGG PATHWAY map by using the convert command of ImageMagick, and coloring according to the coordinate information and the attribution color of the gene, protein or metabolite mapped to the annotated element;

6) editing and modifying KEGG PATHWAY html files according to html rules, modifying the popup title information of the annotated elements into expression or differential expression information of corresponding genes, proteins or metabolites and other accessory information.

Preferably, in step 2), if the upper and lower extreme values of the differential expression are infinite values, replacing the upper and lower extreme values with non-infinite maximum values or non-infinite minimum values; and if the upper extreme value and the lower extreme value of the differential expression are non-integers, rounding the minimum value downwards, and rounding the maximum value upwards.

Preferably, in step 5), a scale is drawn at the upper blank of KEGG PATHWAY map.

Further, the multi-omic method comprises two groups of chemical association methods and three groups of chemical association methods, wherein in the two groups of chemical association methods, after two groups of scales of a proteome and a metabolome or a transcriptome and the metabolome are respectively obtained according to the single omic method and the color information of each gene, protein or metabolite, the coloring of the gene, protein or metabolite, the drawing of a double-color scale and the html file information popup editing are respectively carried out.

Preferably, the two-color scale is arranged in horizontal or vertical rows at the upper margin in KEGG PATHWAY map.

Further, in the two groups of chemical association methods, after acquiring respective color scales and colors of genes and proteins for a proteome and a transcriptome, according to coordinates of annotated elements, left and right averaging is performed on a square frame occupied by the annotated elements in a map or front and back part averaging is performed on a line occupied by the annotated elements in the map, and then coloring, drawing of a double-color scale and html file information popup editing are performed.

Further, in the triomics method, for the proteome, the transcriptome and the metabolome, after respective scales and color information of each gene, protein or metabolite are obtained according to the above-mentioned monoomics method and two sets of chemical association method, drawing of the three-color scales, coloring of the gene, protein or metabolite and html file information popup editing are performed respectively.

Preferably, the three color scales are arranged in horizontal or vertical rows at the upper margin in KEGG PATHWAY map.

According to another aspect of the present invention, the present invention provides the application of the method for personalized display of the above-mentioned monoomics and multinomial KEGG PATHWAY map expression heatmaps to visually display (differential) expression levels of genes, proteins or metabolites in the monoomics and multinomics.

The innovation of the invention is that in the KEGG PATHWAY map with multiple sets of chemical associations, the expression, difference level and significance of each omics element in each KEGG PATHWAY map are simultaneously and massively displayed in a color scale, element filling color, element graph display mode and the like. The defects that the existing related software only can display a single omics element expression heat map and is not easy to edit, modify and individually display are overcome, and the defects that the functions of the software cannot be expanded to multi-group chemical association and the expressions and differences of various omics elements with different expression scales cannot be clearly shown are also overcome. The invention is also innovative in that based on the invention, KEGG PATHWAY maps can be expanded in a single-group and multi-group mathematics range, and elements in KEGG PATHWAY maps can be displayed in batch in an individualized way, such as a five-pointed star mark, as shown in fig. 1. Overall, the innovation of the invention is that the method can be processed in batch, can be modified in a personalized way, and can clearly and specifically display the expression and significance of elements in different scales from single-component science to multi-component science in transcription, protein and metabolism.

Drawings

FIG. 1 is an expanded example of KEGG PATHWAY map, in which differentially upregulated genes are labeled with five-pointed stars.

FIG. 2 is an example of the box coordinates occupied by the KEGG PATHWAY map protein or gene of the invention.

FIG. 3 is an example of coordinates of a line segment occupied by the KEGG PATHWAY map protein or gene of the present invention.

FIG. 4 is an example of the circular coordinates occupied by the KEGG PATHWAY map metabolite of the present invention.

FIG. 5 is a graphical representation of the results of a single panel of the KEGG PATHWAY map gene or protein expression heatmap of the invention.

FIG. 6 is a demonstration of the results of editing the popup for KEGG PATHWAY map in the KEGG PATHWAYhtml format in the present invention monoomics.

Figure 7 is a display of the results of a thermomap of the present invention with a combination of the two omics (protein and metabolism or transcription and metabolism) KEGG PATHWAY map genes and protein expression.

Figure 8 is a display of the results of the inventive binary association (protein and metabolism or transcription and metabolism) edited popup for KEGG PATHWAY map in KEGG PATHWAYhtml.

Figure 9 is a block result display of the inventive binary association (protein vs. transcription) KEGG PATHWAY map gene and protein expression heatmap.

Figure 10 is a line-result display of the inventive binary association (protein vs. transcription) KEGG PATHWAY map gene and protein expression heatmap.

Figure 11 is a display of the results of the inventive binary association (protein and transcription) editing a popup for KEGG PATHWAY map in the KEGG PATHWAYhtml format.

FIG. 12 is a display of the results of a three panel summary of the present invention combined with a KEGG PATHWAY map gene, protein and metabolite expression heatmap.

Detailed Description

In order to facilitate understanding of the invention, the invention will be explained in detail below with reference to the accompanying drawings in conjunction with embodiments. It should be noted that, since the drawings in the specification are only shown as black and white drawings, and actual color filling cannot be shown, characters such as "blue", "yellow", "half blue and half pink", and "half red and half pink" are adopted in the drawings to mark the side of some colors to assist in explanation, and the practical application is not limited to this.

EXAMPLE 1 Single chemistry KEGG PATHWAY

The method comprises the following implementation steps:

1) based on the expression information of genes, proteins or metabolites and KEGG PATHWAY annotation information (see Table 1),

a format file (as in table 2) is prepared for each KEGG PATHWAY involved.

TABLE 1 expression information of genes, proteins or metabolites and KEGG PATHWAY annotation information example

gene_id	log2FoldChange	KO	Pathway
				TRINITY_1	-3.02858	K00012	ko00040\|ko00520\|ko00053\|ko00500
TRINITY_2	-1.5612	K01728	ko00040\|ko0204
				TRINITY_3	2.670045	K01051	ko00040\|ko00500
TRINITY_5	3.643347	K00963	ko00040\|ko00520\|ko00500\|ko00052

TABLE 2 preparation Format files for each KEGG PATHWAY referred to in TABLE 1

Html	gene_id	log2FC	up_down	KO
					&#13；	TRINITY_1	-3.02858	Down	K00012
&#13；	TRINITY_2	-1.5612	Down	K01728
					&#13；	TRINITY_3	2.670045	Up	K01051
&#13；	TRINITY_5	3.643347	Up	K00963

2) The integer values (non-integer, minimum rounded down, maximum rounded up) of the upper and lower extremes of expression or differential expression (non-infinite maximum or minimum substituted if infinite) of all genes, proteins or metabolites in each KEGG PATHWAY were obtained (in the example of table 2, maximum 13, minimum 0).

3) The maximum value to the minimum value are equally divided into n equal parts to form an equal difference number sequence from 0 to 13. The scale is given colors, such as a minimum value of blue (#4682B4), a gradual change from blue to gray from the minimum value to the median value, a maximum value of red (# FF0000), and a gradual change from gray to red from the median value to the maximum value.

4) There are n-1 range intervals between the minimum value and the maximum value, and each range interval has one and only one corresponding gradient color. According to the expression or differential expression value of each gene, protein or metabolite under KEGG PATHWAY, matching to the corresponding range interval, and obtaining the corresponding gradient color, as shown in table 3.

Color codes corresponding to the expression or differential expression values of each gene, protein or metabolite in tables 3 and KEGG PATHWAY

Html	gene_id	log2FC	up_down	KO	Color code
						&#13；	TRINITY_1	-3.02858	Down	K00012	#5A8AB1
&#13；	TRINITY_2	-1.5612	Down	K01728	#849AAD
						&#13；	TRINITY_3	2.670045	Up	K01051	#E33535
&#13；	TRINITY_5	3.643347	Up	K00963	#FF0000

5) According to the information of the annotated element (third column in table 1) in KEGG PATHWAY html corresponding to the gene, protein or metabolite (first column in table 1), the coordinates of the annotated element are obtained, and if the protein and the gene are in a box (fixed in length and width) in KEGG PATHWAY map, the coordinates have four coordinates, as shown in fig. 2, and if the protein and the gene are in a line segment, the coordinates have eight coordinates, as shown in fig. 3. Metabolites are small circles (fixed radius) in KEGG PATHWAY map with three coordinate values, as in FIG. 4.

6) After the coordinates are acquired, the genes, proteins or metabolites of the corresponding coordinates are colored using the convert command of imagemap.

7) And drawing a color scale on the map picture after the element is colored according to the gradient and the range of the color scale, and obtaining a result as shown in figure 5.

8) And editing the html file corresponding to the map, and modifying and writing popup window information according to the html writing rule. In this manner, the user can easily and accurately select the desired target,

when the mouse is placed on the upper color element, corresponding expression information and other accessory information are popped up, as shown in fig. 6.

Example 2 protein and metabolism or transcription and metabolism KEGG PATHWAY

The method comprises the following implementation steps:

1) the protein and the metabolism or the gene and the metabolite are selected to be different gradual colors and colored according to the steps 1) to 6) in the example 1.

2) And drawing a double-color scale for the map picture after the element is colored according to the gradient and the color scale range. The results are shown in FIG. 7.

3) And editing the html file corresponding to the map, and modifying and writing popup window information according to the html writing rule. Thus, when the mouse is placed on the upper color element, the corresponding expression information and other auxiliary information are popped up, as shown in fig. 8.

Example 3 proteins and transcripts KEGG PATHWAY

The method comprises the following implementation steps:

1) different gradient color selections were selected for the protein and gene, respectively, according to the steps 1) -4) of example 1.

2) Because the gene corresponds to the same annotated element as the protein it encodes, it occupies the same line or box (coordinates) on the map. For the boxes, because their length and width are fixed (46, 17), they are averaged and the genes on the left half are graded and the proteins on the right half are graded according to the respective coordinates using the convert command of imagemap. For example, if the position coordinate of one box is coords 620,532,666,549, the gene on the coordinate 620,532,643,549 is gradually changed, the protein on 643,532,666,549 is gradually changed, and a color scale is drawn on the map picture after the element is colored according to the gradually changed color and the range of the color scale. As shown in fig. 9. For the line, the principle is the same as that of a square frame, the line is equally divided, the gene on the former part is gradually changed in color, the protein on the latter part is gradually changed in color, and a color scale is drawn on the map picture after the element is colored according to the gradually changed color and the range of the color scale. As shown in fig. 10.

3) And editing the html file corresponding to the map, and modifying and writing popup window information according to the html writing rule. Thus, when the mouse is placed on the upper color element, the corresponding expression information and other auxiliary information are popped up, as shown in fig. 11.

Example 4 Trilogy KEGG PATHWAY

The method comprises the following implementation steps:

1) the protein and the gene are respectively colored by different gradual colors according to the steps 1) to 3) in the example 3, and a color scale is drawn.

2) The metabolites were selected to be colored in a gradient color different from that of the genes and proteins according to the steps 1) to 7) of example 1, and a color scale was drawn. The triad color scales are transversely arranged and are not covered or shielded. As in fig. 12.

3) And editing the html file corresponding to the map, and modifying and writing popup window information according to the html writing rule. Thus, when the mouse is placed on the coloring element, corresponding expression information and other accessory information are popped up.

The foregoing is only a preferred embodiment of the present patent application, and it should be noted that, for those skilled in the art, several modifications and substitutions can be made without departing from the technical principle of the present patent application, and these modifications and substitutions should also be regarded as the protection scope of the present patent application.

Claims

1. The method for individually displaying the KEGG PATHWAY map expression heatmap of the single omics and the multiple groups of studies comprises a single omics method and a multiple groups of studies, wherein the single omics method comprises the following steps:

1) matching the annotation elements to an html file of KEGG PATHWAY according to the expression or differential expression level of the known target gene, protein or metabolite and corresponding annotated elements in KEGG PATHWAY to obtain coordinate information of the annotated elements in a KEGG PATHWAY map picture;

2) for each KEGG PATHWAY annotated by the target gene, protein or metabolite, acquiring the integer values of the upper and lower extreme values of the expression or differential expression level of all genes, proteins or metabolites in KEGG PATHWAY as the upper and lower limits of the color scale of the expression heatmap;

4) matching to a corresponding range interval according to the expression or differential expression level of each gene, protein or metabolite under KEGG PATHWAY to obtain corresponding attribution color;

6) and editing KEGG PATHWAY html files according to html rules, and modifying the popup title information of the annotated elements into expression or differential expression levels of corresponding genes, proteins or metabolites and other accessory information.

2. The method for personalized presentation of an expressed heatmap of unitary and multigroup science KEGG PATHWAY map according to claim 1, wherein in step 2), if the upper and lower extreme values of the differential expression are infinite values, the extreme values are replaced with non-infinite maximum values or non-infinite minimum values; and if the upper extreme value and the lower extreme value of the differential expression are non-integers, rounding the minimum value downwards, and rounding the maximum value upwards.

3. The method for personalized presentation of an omics and multigroup science KEGG PATHWAY map expression heatmap as claimed in claim 1, wherein in step 5), a ruler is drawn at the upper blank of KEGG PATHWAY map.

4. The method for individualized display of monamics and multigroup science KEGG PATHWAY map expression heatmaps according to claim 1, wherein the multiomic method comprises two groups of chemical association methods and three groups of chemical association methods, wherein two groups of respective scales and color information of each gene, protein or metabolite are obtained for proteome and metabolome or transcriptome and metabolome according to the single omic method, and then the genes, proteins or metabolites are colored, the two color scales are drawn, and html file information popup is edited.

5. The method for the personalized presentation of monoomics and multigroup science KEGG PATHWAY map expression heatmaps of claim 4, wherein said two-color scale is arranged in horizontal or vertical rows at the upper margin in KEGG PATHWAY map.

6. The method for individualized display of monamics and multigroup science KEGG PATHWAY map expression heatmaps according to claim 1, wherein the multiomics method comprises two groups of chemical association methods and three groups of chemical association methods, wherein in the two groups of chemical association methods, after acquiring respective color scales and colors of genes and proteins for proteomes and transcriptions, the left and right halves of the square occupied by the annotated elements in the map or the front and back halves of the lines occupied by the annotated elements in the map are equally divided according to the coordinates of the annotated elements, and then the coloring, drawing of double color scales and html document information popup editing are performed.

7. The method of single and multiple schools KEGG PATHWAY map expression heatmap personalized presentation of claim 6, wherein the two color scales are arranged in rows or columns at the upper blank in KEGG PATHWAY map.

8. The method for individualized display of monamics and multigroup science KEGG PATHWAY map expression heatmaps according to claim 4 or 6, wherein in the triomics method, for proteomes, transcriptomes and metabolomes, after obtaining respective scales and color information of each gene, protein or metabolite according to the monamics method and the two-group association method, drawing of the three-color scales, coloring of the gene, protein or metabolite and html file information popup editing are respectively performed.

9. The method for the personalized presentation of omics and multigroup science KEGG PATHWAY map expression heatmaps of claim 8, wherein the three color scales are arranged in horizontal or vertical rows at the upper blank in KEGG PATHWAY map.

10. The use of the method for the personalized presentation of monoomics and multigroup KEGG PATHWAY map expression heatmaps as claimed in any of claims 1 to 9 for the visual display of the differential expression levels of genes, proteins or metabolites in monoomics and multigroup.