Hub Gene Rank

Rank module genes by supplied eigengene connectivity.

Description

A hub ranking orders genes by supplied module connectivity.

A hub ranking orders genes by supplied module connectivity. Connectivity has to be defined upstream; signed values and absolute connectivity are different ranking choices.^[1]

Rank module genes by supplied eigengene connectivity.

When to use Hub Gene Rank

Use this tool to rank module genes by supplied eigengene connectivity.

Prepare the upstream counts, expression values, sequences or record lists requested by this tool. Keep corresponding features in the same order and confirm count units, transformations and caller-selected criteria.

How to use Hub Gene Rank and understand its results

Prepare the upstream counts, expression values, sequences or record lists requested by this tool. Keep corresponding features in the same order and confirm count units, transformations and caller-selected criteria.
Enter geneIds, connectivities, topCount using the field table and calculation rules, then run the tool.
Read topGeneIds, topConnectivities. The explanation below defines the units, signs, ordering and any flags or placeholder values.
If the tool reports an input issue, correct the values and run it again. Apply the stated assumptions when interpreting a successfully returned result.

Input field	Meaning	Value type; see rules below	Requirement
geneIds	Gene ids	list of string	Required
connectivities	Connectivities	list of number	Required
topCount	Top count	number	Required

Enter aligned nonempty IDs/connectivities and a top count between one and the number of genes. Sort the supplied signed values descending and return selected IDs and connectivities. Use an integer count; array slicing truncates a fractional value.

rank descending signed connectivity, breaking ties by input index

Units, indexing, boundary conditions and exceptional cases are defined in the calculation rules above.

Output field	Meaning	Value type
topGeneIds	Top gene ids	list of string
topConnectivities	Top connectivities	list of number

json

{
  "input": {
    "geneIds": [
      "a",
      "b",
      "c"
    ],
    "connectivities": [
      0.1,
      0.8,
      0.4
    ],
    "topCount": 2
  },
  "output": {
    "topGeneIds": [
      "b",
      "c"
    ],
    "topConnectivities": [
      0.8,
      0.4
    ]
  }
}

Limitations and assumptions

The tool does not compute correlations, module membership or connectivity and does not take absolute values. High rank does not prove causal regulatory importance.

Numeric inputs must be finite. Follow the calculation-specific rules for overflow, underflow and exceptional cases. Lists are limited to 100,000 entries; the rules above may require smaller limits. Missing required fields, extra fields, wrong value types and violations of the calculation rules are input errors.

Alternative or Complementary methods

Use Module Eigengene: Extract the leading principal component of a gene-by-sample module. For a complementary task, use WGCNA Power Selector: Select the first WGCNA power meeting a caller-supplied scale-free-fit criterion.

References

Hub Gene Rank — tool.io

Similar or alternative tools

Module Eigengene
Extract the leading principal component of a gene-by-sample module.
WGCNA Power Selector
Select the first WGCNA power meeting a caller-supplied scale-free-fit criterion.