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Module #729, TG: 2.8, TC: 1.2, 97 probes, 95 Entrez genes, 18 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.
cell fraction
A generic term for parts of cells prepared by disruptive biochemical techniques.
cellular_component
The part of a cell or its extracellular environment in which a gene product is located. A gene product may be located in one or more parts of a cell and its location may be as specific as a particular macromolecular complex, that is, a stable, persistent association of macromolecules that function together.
cell
The basic structural and functional unit of all organisms. Includes the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope.
membrane fraction
That fraction of cells, prepared by disruptive biochemical methods, that includes the plasma and other membranes.
insoluble fraction
That fraction of cells, prepared by disruptive biochemical methods, that is not soluble in water.
cell part
Any constituent part of a cell, the basic structural and functional unit of all organisms.
all
This term is the most general term possible
cell part
Any constituent part of a cell, the basic structural and functional unit of all organisms.
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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.
molecular_function
Elemental activities, such as catalysis or binding, describing the actions of a gene product at the molecular level. A given gene product may exhibit one or more molecular functions.
catalytic activity
Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
monooxygenase activity
Catalysis of the incorporation of one atom from molecular oxygen into a compound and the reduction of the other atom of oxygen to water.
oxidoreductase activity
Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen
Catalysis of an oxidation-reduction (redox) reaction in which hydrogen or electrons are transferred from each of two donors, and molecular oxygen is reduced or incorporated into a donor.
oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen
Catalysis of an oxidation-reduction (redox) reaction in which hydrogen or electrons are transferred from reduced flavin or flavoprotein and one other donor, and one atom of oxygen is incorporated into one donor.
all
This term is the most general term possible
oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen
Catalysis of an oxidation-reduction (redox) reaction in which hydrogen or electrons are transferred from reduced flavin or flavoprotein and one other donor, and one atom of oxygen is incorporated into one donor.
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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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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:0005626 | 3.511e-03 | 3.306 | 12
ADORA2A, CYP1A2, CYP3A4, DES, FOLH1, FUT3, SLC11A1, SLC15A1, SLC17A6, SLC30A5, UGT2B28, VAMP2 | 369 | insoluble fraction |
| GO:0005624 | 9.464e-03 | 3.189 | 11
ADORA2A, CYP1A2, CYP3A4, FOLH1, FUT3, SLC11A1, SLC15A1, SLC17A6, SLC30A5, UGT2B28, VAMP2 | 356 | membrane fraction |
| GO:0000267 | 2.272e-02 | 4.192 | 12
ADORA2A, CYP1A2, CYP3A4, DES, FOLH1, FUT3, SLC11A1, SLC15A1, SLC17A6, SLC30A5, UGT2B28, VAMP2 | 468 | cell fraction |
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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:0016712 | 2.387e-03 | 0.05114 | 3
CYP1A2, CYP2B6, CYP3A4 | 6 | oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen |
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KEGG Pathway test for over-representation
HELP
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 |
| 00830 | 2.451e-03 | 0.1719 | 4
CYP1A2, CYP2B6, CYP3A4, UGT2B28 | 21 | Retinol metabolism |
| 00982 | 1.395e-02 | 0.2946 | 4
CYP1A2, CYP2B6, CYP3A4, UGT2B28 | 36 | Drug metabolism - cytochrome P450 |
| 00980 | 1.501e-02 | 0.3028 | 4
CYP1A2, CYP2B6, CYP3A4, UGT2B28 | 37 | Metabolism of xenobiotics by cytochrome P450 |
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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
HELP
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
ACOT11acyl-CoA thioesterase 11 (216103_at), score: 0.91
ADORA2Aadenosine A2a receptor (205013_s_at), score: 0.73
ALDOAP2aldolase A, fructose-bisphosphate pseudogene 2 (211617_at), score: 0.87
ALMS1Alstrom syndrome 1 (214707_x_at), score: 0.89
APBB2amyloid beta (A4) precursor protein-binding, family B, member 2 (212972_x_at), score: 0.81
BCL9B-cell CLL/lymphoma 9 (204129_at), score: 0.72
C17orf86chromosome 17 open reading frame 86 (221621_at), score: 0.78
CATSPER2cation channel, sperm associated 2 (217588_at), score: 0.74
CBFA2T2core-binding factor, runt domain, alpha subunit 2; translocated to, 2 (207625_s_at), score: 0.71
CDKN1Ccyclin-dependent kinase inhibitor 1C (p57, Kip2) (213183_s_at), score: 0.83
CEACAM5carcinoembryonic antigen-related cell adhesion molecule 5 (201884_at), score: 0.72
CEP27centrosomal protein 27kDa (220071_x_at), score: 0.79
CGGBP1CGG triplet repeat binding protein 1 (214050_at), score: 0.77
CHI3L1chitinase 3-like 1 (cartilage glycoprotein-39) (209395_at), score: 0.72
CLEC4EC-type lectin domain family 4, member E (219859_at), score: 0.72
CYP1A2cytochrome P450, family 1, subfamily A, polypeptide 2 (207608_x_at), score: 0.72
CYP2B6cytochrome P450, family 2, subfamily B, polypeptide 6 (217133_x_at), score: 0.84
CYP3A4cytochrome P450, family 3, subfamily A, polypeptide 4 (205998_x_at), score: 0.73
DAPP1dual adaptor of phosphotyrosine and 3-phosphoinositides (219290_x_at), score: 0.94
DAZ1deleted in azoospermia 1 (216922_x_at), score: 0.83
DAZ3deleted in azoospermia 3 (208281_x_at), score: 0.77
DAZ4deleted in azoospermia 4 (216351_x_at), score: 0.84
DESdesmin (216947_at), score: 0.73
DIP2ADIP2 disco-interacting protein 2 homolog A (Drosophila) (215529_x_at), score: 0.77
DKFZp686O1327hypothetical gene supported by BC043549; BX648102 (216877_at), score: 0.87
DLX4distal-less homeobox 4 (208216_at), score: 0.72
DNAH3dynein, axonemal, heavy chain 3 (220725_x_at), score: 0.73
ELK4ELK4, ETS-domain protein (SRF accessory protein 1) (206919_at), score: 0.79
EPB41L1erythrocyte membrane protein band 4.1-like 1 (212339_at), score: 0.83
FAM106Afamily with sequence similarity 106, member A (220575_at), score: 0.73
FAM75A3family with sequence similarity 75, member A3 (215935_at), score: 0.71
FBXO41F-box protein 41 (44040_at), score: 0.86
FBXW12F-box and WD repeat domain containing 12 (215600_x_at), score: 0.73
FCARFc fragment of IgA, receptor for (211305_x_at), score: 0.72
FLJ11292hypothetical protein FLJ11292 (220828_s_at), score: 0.91
FLJ21369hypothetical protein FLJ21369 (220401_at), score: 0.79
FLJ23172hypothetical LOC389177 (217016_x_at), score: 0.87
FOLH1folate hydrolase (prostate-specific membrane antigen) 1 (217487_x_at), score: 0.74
FUT3fucosyltransferase 3 (galactoside 3(4)-L-fucosyltransferase, Lewis blood group) (214088_s_at), score: 0.7
G3BP1GTPase activating protein (SH3 domain) binding protein 1 (222187_x_at), score: 0.98
GK2glycerol kinase 2 (215430_at), score: 0.73
HCG2P7HLA complex group 2 pseudogene 7 (216229_x_at), score: 0.82
IBD12Inflammatory bowel disease 12 (215373_x_at), score: 0.86
KCNJ14potassium inwardly-rectifying channel, subfamily J, member 14 (220776_at), score: 0.71
KCNJ16potassium inwardly-rectifying channel, subfamily J, member 16 (219564_at), score: 0.78
LAMB4laminin, beta 4 (215516_at), score: 0.7
LOC100134401hypothetical protein LOC100134401 (213605_s_at), score: 0.8
LOC51152melanoma antigen (220771_at), score: 0.74
LOC647070hypothetical LOC647070 (215467_x_at), score: 0.79
LOC91316glucuronidase, beta/ immunoglobulin lambda-like polypeptide 1 pseudogene (215816_at), score: 0.71
MAP2K7mitogen-activated protein kinase kinase 7 (216206_x_at), score: 0.81
MEFVMediterranean fever (208262_x_at), score: 0.88
METAP2methionyl aminopeptidase 2 (202015_x_at), score: 0.88
METTL7Amethyltransferase like 7A (211424_x_at), score: 0.97
MFSD11major facilitator superfamily domain containing 11 (221192_x_at), score: 0.73
MLLT10myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 10 (216506_x_at), score: 0.7
NCRNA00092non-protein coding RNA 92 (215861_at), score: 0.76
PDE4Cphosphodiesterase 4C, cAMP-specific (phosphodiesterase E1 dunce homolog, Drosophila) (206792_x_at), score: 0.74
POGZpogo transposable element with ZNF domain (215281_x_at), score: 0.88
POM121L9PPOM121 membrane glycoprotein-like 9 (rat) pseudogene (222253_s_at), score: 0.81
PPARGC1Aperoxisome proliferator-activated receptor gamma, coactivator 1 alpha (219195_at), score: 0.87
PRINSpsoriasis associated RNA induced by stress (non-protein coding) (216051_x_at), score: 0.96
RP3-377H14.5hypothetical LOC285830 (222279_at), score: 0.74
RP5-886K2.1neuronal thread protein AD7c-NTP (207953_at), score: 0.73
RPL21P37ribosomal protein L21 pseudogene 37 (216479_at), score: 0.87
RPL23AP32ribosomal protein L23a pseudogene 32 (207283_at), score: 0.71
RPL35Aribosomal protein L35a (215208_x_at), score: 0.87
SCARF1scavenger receptor class F, member 1 (206995_x_at), score: 0.75
SCD5stearoyl-CoA desaturase 5 (220232_at), score: 0.72
SFTPBsurfactant protein B (214354_x_at), score: 0.87
SH3BP2SH3-domain binding protein 2 (217257_at), score: 0.81
SH3GL3SH3-domain GRB2-like 3 (211565_at), score: 0.79
SLC11A1solute carrier family 11 (proton-coupled divalent metal ion transporters), member 1 (217473_x_at), score: 0.74
SLC15A1solute carrier family 15 (oligopeptide transporter), member 1 (211349_at), score: 0.71
SLC17A6solute carrier family 17 (sodium-dependent inorganic phosphate cotransporter), member 6 (220551_at), score: 0.71
SLC30A5solute carrier family 30 (zinc transporter), member 5 (220181_x_at), score: 0.75
SPINLW1serine peptidase inhibitor-like, with Kunitz and WAP domains 1 (eppin) (206318_at), score: 0.9
SPNsialophorin (206057_x_at), score: 0.83
SPTLC3serine palmitoyltransferase, long chain base subunit 3 (220456_at), score: 1
SYCP1synaptonemal complex protein 1 (206740_x_at), score: 0.74
TBX6T-box 6 (207684_at), score: 0.71
TIMM8Atranslocase of inner mitochondrial membrane 8 homolog A (yeast) (210800_at), score: 0.92
TP53TG3TP53 target 3 (220167_s_at), score: 0.77
TRIM36tripartite motif-containing 36 (219736_at), score: 0.78
UBQLN4ubiquilin 4 (222252_x_at), score: 0.79
UGT2B28UDP glucuronosyltransferase 2 family, polypeptide B28 (211682_x_at), score: 0.83
VAMP2vesicle-associated membrane protein 2 (synaptobrevin 2) (201557_at), score: 0.71
VEZTvezatin, adherens junctions transmembrane protein (207263_x_at), score: 0.81
XRCC2X-ray repair complementing defective repair in Chinese hamster cells 2 (207598_x_at), score: 0.73
ZC3H7Bzinc finger CCCH-type containing 7B (206169_x_at), score: 0.89
ZNF160zinc finger protein 160 (214715_x_at), score: 0.72
ZNF440zinc finger protein 440 (215892_at), score: 0.8
ZNF492zinc finger protein 492 (215532_x_at), score: 0.73
ZNF639zinc finger protein 639 (218413_s_at), score: 0.71
ZNF816Azinc finger protein 816A (217541_x_at), score: 0.88
Non-Entrez genes
215816_atUnknown, score: 0.85
207625_s_atUnknown, score: 0.73
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-GEOD-4219-raw-cel-1311956824.cel | 24 | 7 | Sph-mono | hgu133plus2 | none | Sph-mon 1 |
| E-GEOD-4219-raw-cel-1311956358.cel | 10 | 7 | Sph-mono | hgu133plus2 | none | Sph-mon 1 |
| E-TABM-263-raw-cel-1515485651.cel | 1 | 6 | Cycle | hgu133a2 | none | Cycle 1 |
| E-GEOD-4219-raw-cel-1311956178.cel | 6 | 7 | Sph-mono | hgu133plus2 | none | Sph-mon 1 |
| 46A.CEL | 1 | 3 | DS-mosaic | hgu133plus2 | none | DS-mosaic 1 |
| E-TABM-263-raw-cel-1515485831.cel | 10 | 6 | Cycle | hgu133a2 | none | Cycle 1 |
| t21d 08-03.CEL | 7 | 1 | DS-CC | hgu133a | Down | DS-CC 7 |
| 3Twin.CEL | 3 | 2 | DS-twin | hgu133plus2 | Down | DS-twin 3 |
| ctrl c 08-03.CEL | 3 | 1 | DS-CC | hgu133a | none | DS-CC 3 |
| 2Twin.CEL | 2 | 2 | DS-twin | hgu133plus2 | none | DS-twin 2 |
| E-GEOD-3407-raw-cel-1437949557.cel | 1 | 4 | Cockayne | hgu133a | CS | eGFP |
| ctrl a 08-03.CEL | 1 | 1 | DS-CC | hgu133a | none | DS-CC 1 |
| E-GEOD-4219-raw-cel-1311956275.cel | 8 | 7 | Sph-mono | hgu133plus2 | none | Sph-mon 1 |
| E-GEOD-4219-raw-cel-1311956398.cel | 12 | 7 | Sph-mono | hgu133plus2 | none | Sph-mon 1 |
| E-GEOD-4219-raw-cel-1311956138.cel | 4 | 7 | Sph-mono | hgu133plus2 | none | Sph-mon 1 |
| E-GEOD-4219-raw-cel-1311956634.cel | 19 | 7 | Sph-mono | hgu133plus2 | none | Sph-mon 1 |
| t21a 08-03.CEL | 4 | 1 | DS-CC | hgu133a | Down | DS-CC 4 |
| E-GEOD-4219-raw-cel-1311956083.cel | 2 | 7 | Sph-mono | hgu133plus2 | none | Sph-mon 1 |
© 2008-2010 Computational Biology Group, Department of Medical Genetics,
University of Lausanne, Switzerland
