Data Preparation

AIPA supports three different inputs, each input supports analysis with different methods:

Gene list: Over-representation analysis (ORA)
Gene list and fold change: Kolmogorov-Smirnov test (KS Test), Wilcoxon signed-rank test (Wilcox Test), Fast Pre-ranked Gene Set Enrichment Analysis (FGSEA)
Expression data matrix: ORA, KS test, Wilcox test, FGSEA, GSA (Geneset Analysis), Gene Set Enrichment Analysis (GSEA), Pathway Analysis with Down-weighting of Overlapping Genes (PADOG)

Gene list

Input gene list must be stored in a .txt file with each gene on a separate line. line. The Gene ID can be EntrezID, KEGG ID, Gene Symbol, etc.

Below are examples with GeneID (EntreID), Gene Symbol, KEGG ID, and Affymetrix hgu133plus2 probe.

LRRC47
LZTS2
MAD2L1
MAP1B
MAP2
MAP2K3
MAP2K4
MAP2K7
MAPK9
MARK4

hsa:1720
hsa:989
hsa:3608
hsa:4720
hsa:6439
hsa:5897
hsa:9480
hsa:1164
hsa:6229
hsa:8487

1552256_a_at
1552257_a_at
1552258_at
1552261_at
1552263_at
1552264_a_at
1552266_at
1552269_at
1552271_at
1552272_a_at 

Gene list and fold change

Input gene list must be stored in a .txt or .tsv file with each gene and its fold change on each line separated by a tab character. Gene ID can be EntrezID, KEGG ID, Gene Symbol, etc. To see all supported ID Types, please visit the Data source page.

Below are examples with GeneID (EntreID), Gene Symbol, KEGG ID, and Affymetrix hgu133plus2 probe.

23020 -0.022104449 55644 -0.023851675 55072 -0.020101857 2563 0.029127045 22976 0.018797544 2300 0.023799038 10936 -0.029220944 2963 0.014374435 23127 0.051962119 55423 0.03010304823020	ABHD4 0.220127184768263 ABHD5 0.615439683590562 ABHD6 1.50831660795693 ABHD8 -0.281072224128675 ABI1 0.426171730503105 ABI2 -0.260226045229052 ABL1 0.595988333627509 ABL2 -0.00671259418579993 ABLIM1 0.805408665490459 ABLIM2 2.44735717462544
hsa:10625 -0.001011359 hsa:6795 0.000978679 hsa:64109 0.001007177 hsa:23051 0.000637776 hsa:79726 0.001316198 hsa:6503 0.000699499 hsa:55026 -0.00062984 hsa:114883 0.001487218 hsa:9310 0.000528979 hsa:10137 0.000463783	1552311_a_at -0.838394204314119 1552312_a_at 2.7864702280181 1552314_a_at 0.828274229038452 1552315_at -0.025119056689585 1552316_a_at -0.0591446125739281 1552318_at 1.19103929628282 1552319_a_at -0.226665137288169 1552320_a_at 0.200855604759189 1552321_a_at 1.4071733409876 1552322_at 0.595988333627509

Expression data file

Expression data can be uploaded manually. Data uploaded from local machines must follow our format (see Data format tab).

Two files are required to perform pathway analysis: 1) Expression data file and 2) Group data file. Both files are in .csv format.

Gene expression data must be saved as a .csv file, in which rows indicate genes and columns indicate samples.
The first row must be sample names and the first column must be genes id.
Sample names should not contain special characters
Gene ID can be EntrezID, KEGG ID, Gene Symbol, etc. To see all support ID types, please visit the Data source page.
It is up to users to normalize expression data before uploading to the website.

Example below is an expression matrix with KEGG ID:

"","GSM21203","GSM21206","GSM21207","GSM21215","GSM21217","GSM21218"
"hsa:10",6.18613917271151,5.64502567098228,6.73324685452829,6.17996658966757,6.50537402264283,6.09164376091985
"hsa:100",6.43032504687542,5.79359967573988,6.63037835414765,6.01262616580018,6.24935089994504,5.9438166716528
"hsa:1000",7.56614063766587,8.27120014366728,7.85361733226786,7.76593559015308,7.8274078562957,7.74649475298197
"hsa:10000",8.527515688339,8.31085197640384,8.05190926233479,8.10895984615411,8.19694107154907,8.31956731386563
"hsa:100008586",4.76648431861781,4.58511764880759,5.13594085162142,4.87417176001213,4.61645421365085,4.55003201505522
"hsa:10001",4.79196585202759,4.91675543877265,4.4863946849729,4.67166475145703,4.71566723642853,5.04455411893207
"hsa:10002",4.61571716066639,4.25217930328034,5.00458346728788,4.54007171613674,4.45401539657362,4.48764759569785
"hsa:10003",3.86808984905074,3.8899102742205,4.02302238911423,4.10485504166507,4.09275831103573,4.07127375991903

Group Data

Sample group data file is optional. However, a predefined sample group file will help selecting samples for analysis faster.
If no group data file is uploaded, users are required to manually select samples for analysis.
Group data file must be saved as a .csv file, in which each row indicates one sample and their groups.
One sample can have multiple groups separated by ,.

Example:

"GSM21203","condition"
"GSM21206","condition"
"GSM21207","condition"
"GSM21215","control"
"GSM21217","control"
"GSM21218","control"

Last modified: 22 December 2024