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Module #479, TG: 3.2, TC: 1.6, 60 probes, 60 Entrez genes, 10 conditions
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The image plot shows the color-coded level of gene expression, for the
genes and conditions in a given transcription module. The genes are on
the horizontal, the conditions on the vertical axis.
The genes are ordered according to their ISA gene scores, similarly
the conditions are ordered according to their condition scores. The
score of a gene means the «degree of inclusion» in
the module: a high score gene is essential in the module.
Condition scores can also be negative, that means that the genes of
the module are all down-regulated in the condition. Here the absolute
value of the score gives the «degree of inclusion».
The plots above and beside the expression matrix show the gene scores
and condition scores, respectively.
Note that the plot is interactive, you can see the name of the gene
and condition under the mouse cursor.
The expression matrix was normalized to have mean zero and standard
deviation one for every gene separately across all conditions
(i.e. not just for the conditions in the module).
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Under-expression is coded with green,
over-expression with red color.
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The GO tree — Biological processes
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This is one of three sections showing Gene Ontology enrichment of the
current module: in this case for biological processes.
The graph shows the hierarchy of the GO categories, their enrichment
for the current module is color coded, and the blue number beside the
category is the minus log ten p-value of the enrichment. (Calculated
using the standard hypergeometric test.) The color of the arrows code
«is a» (cyan) and «part of» relationships.
The tree was built the following way. First all GO terms with more
significant enrichment p-value than 0.05 were collected. Then all
paths from these terms to the root node of the GO tree were included
too. If a GO term is included more than once in the tree, then the
green numbers show 1) the id of the node, this makes it easier to find
other appereances of the term, and 2) the number of appearences.
Note that the same GO category might show up on the graph many
times. This is because the GO was «straightened» for this
graph, i.e. if there are more paths from a GO term to the root node of
the tree, all of them are included. The green numbers
Move the mouse cursor over the terms to get their definition. Clicking
on them takes you to the corresponding Gene Ontology web page.
If you cannot see a graph here at all, that means that there were no
significantly enriched GO categories, at the 0.05 level.
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The GO tree — Cellular Components
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This is one of three sections showing Gene Ontology enrichment of the
current module: in this case for cellular components.
The graph shows the hierarchy of the GO categories, their enrichment
for the current module is color coded, and the blue number beside the
category is the minus log ten p-value of the enrichment. (Calculated
using the standard hypergeometric test.) The color of the arrows code
«is a» (cyan) and «part of» relationships.
The tree was built the following way. First all GO terms with more
significant enrichment p-value than 0.05 were collected. Then all
paths from these terms to the root node of the GO tree were included
too. If a GO term is included more than once in the tree, then the
green numbers show 1) the id of the node, this makes it easier to find
other appereances of the term, and 2) the number of appearences.
Note that the same GO category might show up on the graph many
times. This is because the GO was «straightened» for this
graph, i.e. if there are more paths from a GO term to the root node of
the tree, all of them are included. The green numbers
Move the mouse cursor over the terms to get their definition. Clicking
on them takes you to the corresponding Gene Ontology web page.
If you cannot see a graph here at all, that means that there were no
significantly enriched GO categories, at the 0.05 level.
— Click on the Help button again to close this help window.
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The GO tree — Molecular Function
HELP
This is one of three sections showing Gene Ontology enrichment of the
current module: in this case for molecular function.
The graph shows the hierarchy of the GO categories, their enrichment
for the current module is color coded, and the blue number beside the
category is the minus log ten p-value of the enrichment. (Calculated
using the standard hypergeometric test.) The color of the arrows code
«is a» (cyan) and «part of» relationships.
The tree was built the following way. First all GO terms with more
significant enrichment p-value than 0.05 were collected. Then all
paths from these terms to the root node of the GO tree were included
too. If a GO term is included more than once in the tree, then the
green numbers show 1) the id of the node, this makes it easier to find
other appereances of the term, and 2) the number of appearences.
Note that the same GO category might show up on the graph many
times. This is because the GO was «straightened» for this
graph, i.e. if there are more paths from a GO term to the root node of
the tree, all of them are included. The green numbers
Move the mouse cursor over the terms to get their definition. Clicking
on them takes you to the corresponding Gene Ontology web page.
If you cannot see a graph here at all, that means that there were no
significantly enriched GO categories, at the 0.05 level.
— Click on the Help button again to close this help window.
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GO BP test for over-representation
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List of all enriched GO categories (biological processes), at the 0.05
p-value level.
The columns:
- ExpCount is the expected count of genes in the
module annotated with the given GO term, just by chance.
- Count
is the number of genes in the module annotated with the given GO
term.
- Size is the total number of genes (in our universe)
annotated with the GO term.
Clicking on Count shows the genes that drive the
enrichment. You can also click on the individual numbers in
the Count column, to show the driving genes for that individual
GO category.
Clicking on the GO identifiers takes you to the Gene Ontology web
pages.
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| Id | Pvalue | ExpCount | Count | Size | Term |
| GO:0006952 | 4.115e-02 | 1.536 | 7
ADORA1, DMBT1, HAMP, ITGAL, LILRB3, SAA4, SIGLEC1 | 257 | defense response |
| GO:0042730 | 4.909e-02 | 0.0478 | 2
F11, TMPRSS6 | 8 | fibrinolysis |
| GO:0050896 | 4.920e-02 | 7.918 | 17
ADORA1, ATM, CD79B, DMBT1, F11, HAMP, HLA-DQB1, ITGAL, LILRA5, LILRB3, MYO15A, PKLR, PXN, RBM38, SAA4, SIGLEC1, TMPRSS6 | 1325 | response to stimulus |
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GO CC test for over-representation
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List of all enriched GO categories (cellular components), at the 0.05
p-value level.
The columns:
- ExpCount is the expected count of genes in the
module annotated with the given GO term, just by chance.
- Count
is the number of genes in the module annotated with the given GO
term.
- Size is the total number of genes (in our universe)
annotated with the GO term.
Clicking on Count shows the genes that drive the
enrichment. You can also click on the individual numbers in
the Count column, to show the driving genes for that individual
GO category.
Clicking on the GO identifiers takes you to the Gene Ontology web
pages.
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| Id | Pvalue | ExpCount | Count | Size | Term |
| GO:0005886 | 3.028e-02 | 9.377 | 19
ABCA7, ADORA1, ALPPL2, CD79B, CNNM3, FLRT3, GPR144, HLA-DQB1, IL9R, ITGAL, LILRB3, OPRL1, PXN, RASGRP3, SEPT5, SIGLEC1, SLC5A5, SORBS1, TMPRSS6 | 1409 | plasma membrane |
| GO:0005576 | 3.187e-02 | 4.479 | 12
DMBT1, DSPP, F11, FLRT3, HAMP, IGHG1, IL9R, LILRA5, MUC5AC, PRLH, SAA4, SIGLEC1 | 673 | extracellular region |
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GO MF test for over-representation
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List of all enriched GO categories (molecular function), at the 0.05
p-value level.
The columns:
- ExpCount is the expected count of genes in the
module annotated with the given GO term, just by chance.
- Count
is the number of genes in the module annotated with the given GO
term.
- Size is the total number of genes (in our universe)
annotated with the GO term.
Clicking on Count shows the genes that drive the
enrichment. You can also click on the individual numbers in
the Count column, to show the driving genes for that individual
GO category.
Clicking on the GO identifiers takes you to the Gene Ontology web
pages.
— Click on the Help button again to close this help window.
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KEGG Pathway test for over-representation
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List of all enriched KEGG pathways, at the 0.05
p-value level.
The columns:
- ExpCount is the expected count of genes in the
module annotated with the given KEGG pathway, just by chance.
- Count
is the number of genes in the module annotated with the given KEGG
pathway.
- Size is the total number of genes (in our universe)
annotated with the KEGG pathway.
Clicking on Count shows the genes that drive the
enrichment. You can also click on the individual numbers in
the Count column, to show the driving genes for that individual
KEGG pathway.
Clicking on the KEGG identifiers takes you to the KEGG web site.
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| Id | Pvalue | ExpCount | Count | Size | Term |
| 04662 | 4.819e-02 | 0.4546 | 4
CD79B, LILRB3, PTPN6, RASGRP3 | 47 | B cell receptor signaling pathway |
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miRNA test for over-representation
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List of all enriched miRNA families, at the 0.05
p-value level.
The columns:
- ExpCount is the expected count of genes in the
module regulated by the given miRNA family, just by chance.
- Count
is the number of genes in the module regulated by the given miRNA
family.
- Size is the total number of genes (in our universe)
regulated with the given miRNA family.
Clicking on Count shows the genes that drive the
enrichment. You can also click on the individual numbers in
the Count column, to show the driving genes for that individual
miRNA family.
The miRNA regulation data was taken from the TargetScan database.
(Only the conserved sites were used for the current analysis.)
Clicking on the miRNA names takes you to the TargetScan web site.
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Chromosome test for over-representation
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List of all enriched Chromosomes, at the 0.05
p-value level.
The columns:
- ExpCount is the expected number of genes in the
module on the given chromosome, just by chance.
- Count
is the number of genes in the module on the given chromosome.
- Size is the total number of genes (in our universe)
on the given chromosome.
Clicking on Count shows the genes that drive the
enrichment. You can also click on the individual numbers in
the Count column, to show the driving genes for that individual
chromosome.
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A list of all genes in the current module, in alphabetical order. The
size of the text corresponds to the gene scores.
Note that some gene symbols may show up more than once, if many
probes match the same Entrez gene.
Genes with no Entrez mapping are given separately, with their
Affymetrics probe ID.
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Entrez genes
ABCA7ATP-binding cassette, sub-family A (ABC1), member 7 (219577_s_at), score: 0.9
ADORA1adenosine A1 receptor (216220_s_at), score: 0.78
ALDH1L1aldehyde dehydrogenase 1 family, member L1 (215798_at), score: 0.69
ALPPL2alkaline phosphatase, placental-like 2 (216377_x_at), score: 0.72
ATMataxia telangiectasia mutated (210858_x_at), score: 0.69
C2orf37chromosome 2 open reading frame 37 (220172_at), score: -0.88
C7orf58chromosome 7 open reading frame 58 (220032_at), score: -0.73
CCDC40coiled-coil domain containing 40 (220592_at), score: 0.9
CD79BCD79b molecule, immunoglobulin-associated beta (205297_s_at), score: 0.8
CNNM3cyclin M3 (220739_s_at), score: -0.72
CYP3A4cytochrome P450, family 3, subfamily A, polypeptide 4 (205998_x_at), score: 0.74
CYTH4cytohesin 4 (219183_s_at), score: 0.75
DMBT1deleted in malignant brain tumors 1 (208250_s_at), score: 0.8
DSPPdentin sialophosphoprotein (221681_s_at), score: 0.78
F11coagulation factor XI (206610_s_at), score: 0.72
FKBP10FK506 binding protein 10, 65 kDa (219249_s_at), score: 1
FLCNfolliculin (215645_at), score: 0.74
FLRT3fibronectin leucine rich transmembrane protein 3 (219250_s_at), score: -0.77
GBA3glucosidase, beta, acid 3 (cytosolic) (219954_s_at), score: 0.77
GNL3LPguanine nucleotide binding protein-like 3 (nucleolar)-like pseudogene (220716_at), score: 0.68
GPR144G protein-coupled receptor 144 (216289_at), score: 0.9
HAB1B1 for mucin (215778_x_at), score: 0.92
HAMPhepcidin antimicrobial peptide (220491_at), score: 0.68
HLA-DQB1major histocompatibility complex, class II, DQ beta 1 (211654_x_at), score: 0.68
IGHG1immunoglobulin heavy constant gamma 1 (G1m marker) (211693_at), score: 0.9
IL9Rinterleukin 9 receptor (217212_s_at), score: 0.78
INAinternexin neuronal intermediate filament protein, alpha (204465_s_at), score: -0.72
ITGALintegrin, alpha L (antigen CD11A (p180), lymphocyte function-associated antigen 1; alpha polypeptide) (213475_s_at), score: 0.88
LILRA5leukocyte immunoglobulin-like receptor, subfamily A (with TM domain), member 5 (215838_at), score: 0.83
LILRB3leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 3 (211133_x_at), score: 0.76
LOC149478hypothetical protein LOC149478 (215462_at), score: 0.81
MAPK8IP1mitogen-activated protein kinase 8 interacting protein 1 (213013_at), score: 0.7
MOCS1molybdenum cofactor synthesis 1 (211673_s_at), score: 0.76
MUC5ACmucin 5AC, oligomeric mucus/gel-forming (217182_at), score: 0.74
MYO15Amyosin XVA (220288_at), score: 0.71
NOVA2neuro-oncological ventral antigen 2 (206477_s_at), score: 0.73
OPRL1opiate receptor-like 1 (206564_at), score: 0.71
PKLRpyruvate kinase, liver and RBC (222078_at), score: 0.79
PNMAL1PNMA-like 1 (218824_at), score: -0.74
POM121L2POM121 membrane glycoprotein-like 2 (rat) (216582_at), score: 0.86
PRLHprolactin releasing hormone (221443_x_at), score: 0.69
PTPN6protein tyrosine phosphatase, non-receptor type 6 (206687_s_at), score: 0.81
PXNpaxillin (211823_s_at), score: -0.78
RASGRP3RAS guanyl releasing protein 3 (calcium and DAG-regulated) (205801_s_at), score: -0.83
RBM38RNA binding motif protein 38 (212430_at), score: 0.69
RNF121ring finger protein 121 (219021_at), score: 0.76
RPL18AP6ribosomal protein L18a pseudogene 6 (216383_at), score: 0.7
SAA4serum amyloid A4, constitutive (207096_at), score: 0.69
SEPT5septin 5 (209767_s_at), score: 0.74
SIGLEC1sialic acid binding Ig-like lectin 1, sialoadhesin (44673_at), score: 0.67
SLC5A5solute carrier family 5 (sodium iodide symporter), member 5 (211123_at), score: 0.71
SORBS1sorbin and SH3 domain containing 1 (218087_s_at), score: 0.72
ST8SIA3ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 3 (208064_s_at), score: 0.84
TAF15TAF15 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 68kDa (202840_at), score: 0.76
TMCC2transmembrane and coiled-coil domain family 2 (213096_at), score: 0.68
TMPRSS6transmembrane protease, serine 6 (214955_at), score: 0.8
TMSB4Ythymosin beta 4, Y-linked (206769_at), score: 0.8
TNK1tyrosine kinase, non-receptor, 1 (217149_x_at), score: 0.76
TULP2tubby like protein 2 (206733_at), score: 0.84
YPEL1yippee-like 1 (Drosophila) (206063_x_at), score: 0.74
Non-Entrez genes
Unknown, score:
HELP
Conditions in the module, given in the same order as on the expression
plot above. Red color means over-expression, green under-expression in
the given condition.
The barplot below shows the condition (sample) scores. A separate bar
is shown for each sample, its height is the corresponding score of the
sample in the module. The red and green numbers on the bars are the
sample scores expressed in percents, i.e. 100% is 1.0.
The red and green lines show the module thresholds, samples above
the red line and below the green line are included in the module.
The different experiments that were part of the study, are separated
by dashed vertical lines.
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| Id | sample | Experiment | ExpName | Array | Syndrome | Cell.line |
| E-TABM-263-raw-cel-1515485711.cel | 4 | 6 | Cycle | hgu133a2 | none | Cycle 1 |
| E-TABM-263-raw-cel-1515485951.cel | 16 | 6 | Cycle | hgu133a2 | none | Cycle 1 |
| E-TABM-263-raw-cel-1515486111.cel | 24 | 6 | Cycle | hgu133a2 | none | Cycle 1 |
| E-TABM-263-raw-cel-1515485871.cel | 12 | 6 | Cycle | hgu133a2 | none | Cycle 1 |
| E-TABM-263-raw-cel-1515485691.cel | 3 | 6 | Cycle | hgu133a2 | none | Cycle 1 |
| E-TABM-263-raw-cel-1515486131.cel | 25 | 6 | Cycle | hgu133a2 | none | Cycle 1 |
| E-TABM-263-raw-cel-1515486171.cel | 27 | 6 | Cycle | hgu133a2 | none | Cycle 1 |
| E-TABM-263-raw-cel-1515486431.cel | 40 | 6 | Cycle | hgu133a2 | none | Cycle 1 |
| E-TABM-263-raw-cel-1515485671.cel | 2 | 6 | Cycle | hgu133a2 | none | Cycle 1 |
| E-TABM-263-raw-cel-1515485931.cel | 15 | 6 | Cycle | hgu133a2 | none | Cycle 1 |
© 2008-2010 Computational Biology Group, Department of Medical Genetics,
University of Lausanne, Switzerland
