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Module #678, TG: 2.8, TC: 1.4, 103 probes, 103 Entrez genes, 14 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
HELP
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:0010552 | 3.599e-02 | 0.1727 | 3
NR1H3, PPARG, TP53 | 15 | positive regulation of specific transcription from RNA polymerase II promoter |
| GO:0032501 | 4.719e-02 | 18.97 | 32
ACTC1, ADORA2B, ANGPTL2, BDKRB2, BIN1, BTG2, DCLK1, DHRS3, EFNA5, GDF5, GMCL1, HGF, IRF1, KAL1, LDLR, LIN7B, MC4R, MMP10, MMP16, MSX2, NEFM, NPTX1, NR1H3, PPARG, PPL, ROR2, SECTM1, SIX2, SSTR1, TBC1D8, TLR3, TP53 | 1648 | multicellular organismal process |
| GO:0007154 | 4.757e-02 | 22.42 | 36
ADORA2B, ANGPTL2, ANK2, ARHGEF3, ARL4C, ASAP3, BDKRB2, BRIP1, CALCOCO1, CDKN1C, DAPK1, DCLK1, EFNA5, GDF5, GOLT1B, HGF, LIN7B, LOC399491, LRP8, MC4R, MSX2, MX1, NPTX1, P2RY5, PPARG, RASSF2, RCAN2, ROR2, SECTM1, SSTR1, TBC1D2B, TBC1D8, TENC1, TLR3, TNFAIP6, TP53 | 1947 | cell communication |
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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:0031225 | 2.531e-02 | 0.4477 | 4
EFNA5, NTM, OPCML, ULBP2 | 39 | anchored to membrane |
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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.
| Id | Pvalue | ExpCount | Count | Size | Term |
| GO:0030229 | 1.356e-02 | 0.02173 | 2
LDLR, LRP8 | 2 | very-low-density lipoprotein receptor activity |
| GO:0034189 | 1.356e-02 | 0.02173 | 2
LDLR, LRP8 | 2 | very-low-density lipoprotein binding |
| GO:0008528 | 1.356e-02 | 0.2607 | 4
BDKRB2, MC4R, OPCML, SSTR1 | 24 | peptide receptor activity, G-protein coupled |
| GO:0001653 | 2.158e-02 | 0.3042 | 4
BDKRB2, MC4R, OPCML, SSTR1 | 28 | peptide receptor activity |
| GO:0004888 | 2.294e-02 | 3.629 | 12
ADORA2B, BDKRB2, LDLR, LRP8, MC4R, OPCML, P2RY5, PPARG, ROR2, SSTR1, TLR3, ULBP2 | 334 | transmembrane receptor activity |
| GO:0004930 | 4.764e-02 | 1.488 | 7
ADORA2B, BDKRB2, MC4R, OPCML, P2RY5, PPARG, SSTR1 | 137 | G-protein coupled receptor activity |
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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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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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HELP
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
ABCA8ATP-binding cassette, sub-family A (ABC1), member 8 (204719_at), score: 0.7
ACTC1actin, alpha, cardiac muscle 1 (205132_at), score: -0.76
ACTR3BARP3 actin-related protein 3 homolog B (yeast) (218868_at), score: -0.71
ADH1Balcohol dehydrogenase 1B (class I), beta polypeptide (209612_s_at), score: 0.95
ADORA2Badenosine A2b receptor (205891_at), score: 0.79
AIM1absent in melanoma 1 (212543_at), score: 0.78
AKR1C3aldo-keto reductase family 1, member C3 (3-alpha hydroxysteroid dehydrogenase, type II) (209160_at), score: 0.8
ANGPTL2angiopoietin-like 2 (213001_at), score: 0.95
ANK2ankyrin 2, neuronal (202920_at), score: 0.74
ANXA10annexin A10 (210143_at), score: -0.86
APOL6apolipoprotein L, 6 (219716_at), score: 0.72
ARHGEF3Rho guanine nucleotide exchange factor (GEF) 3 (218501_at), score: 0.76
ARL4CADP-ribosylation factor-like 4C (202207_at), score: 0.68
ASAP3ArfGAP with SH3 domain, ankyrin repeat and PH domain 3 (219103_at), score: 0.79
ATP6V0BATPase, H+ transporting, lysosomal 21kDa, V0 subunit b (200078_s_at), score: -0.77
BDKRB2bradykinin receptor B2 (205870_at), score: 0.75
BIN1bridging integrator 1 (210201_x_at), score: 0.78
BRIP1BRCA1 interacting protein C-terminal helicase 1 (221703_at), score: -0.72
BTG2BTG family, member 2 (201236_s_at), score: 0.82
C13orf15chromosome 13 open reading frame 15 (218723_s_at), score: 0.92
CALCOCO1calcium binding and coiled-coil domain 1 (209002_s_at), score: 0.76
CCNG1cyclin G1 (208796_s_at), score: 0.68
CDKN1Ccyclin-dependent kinase inhibitor 1C (p57, Kip2) (213348_at), score: 0.8
CLIP3CAP-GLY domain containing linker protein 3 (212358_at), score: 0.77
CRBNcereblon (218142_s_at), score: 0.69
CRTC3CREB regulated transcription coactivator 3 (218648_at), score: 0.85
DAAM2dishevelled associated activator of morphogenesis 2 (212793_at), score: 0.69
DAPK1death-associated protein kinase 1 (203139_at), score: 0.83
DCLK1doublecortin-like kinase 1 (205399_at), score: 0.85
DENND2ADENN/MADD domain containing 2A (53991_at), score: 0.76
DHRS3dehydrogenase/reductase (SDR family) member 3 (202481_at), score: 0.72
DNAJB9DnaJ (Hsp40) homolog, subfamily B, member 9 (202843_at), score: -0.71
DOCK10dedicator of cytokinesis 10 (219279_at), score: -0.75
EFNA5ephrin-A5 (214036_at), score: 0.69
ENOX1ecto-NOX disulfide-thiol exchanger 1 (219501_at), score: 0.85
GALNT12UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 12 (GalNAc-T12) (218885_s_at), score: 0.72
GDF5growth differentiation factor 5 (206614_at), score: 0.71
GKglycerol kinase (207387_s_at), score: -0.77
GK3Pglycerol kinase 3 pseudogene (215966_x_at), score: -0.8
GLTSCR2glioma tumor suppressor candidate region gene 2 (217807_s_at), score: 0.68
GMCL1germ cell-less homolog 1 (Drosophila) (218458_at), score: -0.74
GOLT1Bgolgi transport 1 homolog B (S. cerevisiae) (218193_s_at), score: -0.72
GTF2A1Lgeneral transcription factor IIA, 1-like (213413_at), score: 0.96
HERC6hect domain and RLD 6 (219352_at), score: 0.71
HGFhepatocyte growth factor (hepapoietin A; scatter factor) (209960_at), score: 0.68
HSD17B7hydroxysteroid (17-beta) dehydrogenase 7 (220081_x_at), score: 0.71
HSPA12Aheat shock 70kDa protein 12A (214434_at), score: 0.74
IFIH1interferon induced with helicase C domain 1 (219209_at), score: 0.91
IRF1interferon regulatory factor 1 (202531_at), score: 0.82
KAL1Kallmann syndrome 1 sequence (205206_at), score: -0.77
KIAA1305KIAA1305 (220911_s_at), score: 0.81
KLHL23kelch-like 23 (Drosophila) (213610_s_at), score: -0.76
LDLRlow density lipoprotein receptor (202068_s_at), score: 0.73
LIN7Blin-7 homolog B (C. elegans) (219760_at), score: -0.73
LOC100132540similar to LOC339047 protein (214870_x_at), score: 0.71
LOC339047hypothetical protein LOC339047 (221501_x_at), score: 0.75
LOC399491LOC399491 protein (214035_x_at), score: 0.68
LRP8low density lipoprotein receptor-related protein 8, apolipoprotein e receptor (205282_at), score: -0.74
LSSlanosterol synthase (2,3-oxidosqualene-lanosterol cyclase) (211019_s_at), score: 0.7
MAN1C1mannosidase, alpha, class 1C, member 1 (218918_at), score: 0.99
MC4Rmelanocortin 4 receptor (221467_at), score: -0.78
MMP10matrix metallopeptidase 10 (stromelysin 2) (205680_at), score: -0.75
MMP16matrix metallopeptidase 16 (membrane-inserted) (207012_at), score: -0.79
MSTO1misato homolog 1 (Drosophila) (218296_x_at), score: -0.81
MSX2msh homeobox 2 (210319_x_at), score: 0.7
MX1myxovirus (influenza virus) resistance 1, interferon-inducible protein p78 (mouse) (202086_at), score: 0.71
MX2myxovirus (influenza virus) resistance 2 (mouse) (204994_at), score: 0.91
NEFMneurofilament, medium polypeptide (205113_at), score: -0.95
NPIPnuclear pore complex interacting protein (204538_x_at), score: 0.72
NPTX1neuronal pentraxin I (204684_at), score: -0.75
NR1H3nuclear receptor subfamily 1, group H, member 3 (203920_at), score: 0.7
NTMneurotrimin (222020_s_at), score: -0.74
OAS22'-5'-oligoadenylate synthetase 2, 69/71kDa (204972_at), score: 0.86
OPCMLopioid binding protein/cell adhesion molecule-like (214111_at), score: -0.79
ORAI3ORAI calcium release-activated calcium modulator 3 (221864_at), score: 0.83
P2RY5purinergic receptor P2Y, G-protein coupled, 5 (218589_at), score: 0.68
PCDH9protocadherin 9 (219737_s_at), score: -0.84
PPARGperoxisome proliferator-activated receptor gamma (208510_s_at), score: 0.7
PPATphosphoribosyl pyrophosphate amidotransferase (209433_s_at), score: -0.77
PPLperiplakin (203407_at), score: 0.88
RASSF2Ras association (RalGDS/AF-6) domain family member 2 (203185_at), score: 0.79
RCAN2regulator of calcineurin 2 (203498_at), score: 0.75
ROR2receptor tyrosine kinase-like orphan receptor 2 (205578_at), score: 0.77
RP11-345P4.4similar to solute carrier family 35, member E2 (217122_s_at), score: 0.68
RPL13Aribosomal protein L13a (200715_x_at), score: 0.69
SDF2L1stromal cell-derived factor 2-like 1 (218681_s_at), score: -0.73
SECTM1secreted and transmembrane 1 (213716_s_at), score: 0.91
SELENBP1selenium binding protein 1 (214433_s_at), score: 0.75
SESN1sestrin 1 (218346_s_at), score: 0.74
SIX2SIX homeobox 2 (206510_at), score: 0.74
SLC25A13solute carrier family 25, member 13 (citrin) (203775_at), score: -0.79
SSTR1somatostatin receptor 1 (208482_at), score: -0.74
SYNPOsynaptopodin (202796_at), score: 0.74
TBC1D2BTBC1 domain family, member 2B (212796_s_at), score: 0.69
TBC1D8TBC1 domain family, member 8 (with GRAM domain) (204526_s_at), score: 0.88
TENC1tensin like C1 domain containing phosphatase (tensin 2) (212494_at), score: 0.72
TLR3toll-like receptor 3 (206271_at), score: 0.84
TM4SF1transmembrane 4 L six family member 1 (209386_at), score: -0.71
TNFAIP6tumor necrosis factor, alpha-induced protein 6 (206026_s_at), score: 0.73
TP53tumor protein p53 (201746_at), score: 0.81
TRIM21tripartite motif-containing 21 (204804_at), score: 0.71
TSPAN13tetraspanin 13 (217979_at), score: -0.73
ULBP2UL16 binding protein 2 (221291_at), score: -1
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-1515486371.cel | 37 | 6 | Cycle | hgu133a2 | none | Cycle 1 |
| E-TABM-263-raw-cel-1515485771.cel | 7 | 6 | Cycle | hgu133a2 | none | Cycle 1 |
| E-TABM-263-raw-cel-1515485891.cel | 13 | 6 | Cycle | hgu133a2 | none | Cycle 1 |
| E-TABM-263-raw-cel-1515485811.cel | 9 | 6 | Cycle | hgu133a2 | none | Cycle 1 |
| E-TABM-263-raw-cel-1515485751.cel | 6 | 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-1515486431.cel | 40 | 6 | Cycle | hgu133a2 | none | Cycle 1 |
| 2433_CNTL.CEL | 4 | 8 | WBS | hgu133plus2 | none | WBS 1 |
| 8495_CNTL.CEL | 10 | 8 | WBS | hgu133plus2 | none | WBS 1 |
| E-TABM-263-raw-cel-1515485791.cel | 8 | 6 | Cycle | hgu133a2 | none | Cycle 1 |
| E-TABM-263-raw-cel-1515486331.cel | 35 | 6 | Cycle | hgu133a2 | none | Cycle 1 |
| E-TABM-263-raw-cel-1515486311.cel | 34 | 6 | Cycle | hgu133a2 | none | Cycle 1 |
| E-TABM-263-raw-cel-1515486271.cel | 32 | 6 | Cycle | hgu133a2 | none | Cycle 1 |
| E-TABM-263-raw-cel-1515486291.cel | 33 | 6 | Cycle | hgu133a2 | none | Cycle 1 |
© 2008-2010 Computational Biology Group, Department of Medical Genetics,
University of Lausanne, Switzerland
