Discipline of Cancer Biomarkers

Bioinformatics
Ana Lvia Silva Galbiatti Glaucia Maria de Mendona Fernandes
segunda-feira, 30 de janeiro de 2012 09:36

1 - What was the name of the platform used for this study? Provide details of the platform used in the study and the basis of selection of the platform used. We enter the site: http://www.ncbi.nlm.nih.gov/pubmed/ in the field of choices fordatabases, we chose the GEO DataSets database, the search field, put the datasetsent by Professor GDS1989 and click search to start the search.

On the next page enter the following to search GeoDataSet Platform

We find the following information in the window:

Pgina 1 de Nova Seo 1

We find the following information in the window:

We enter the link in the platform that took us to a window with several information about the platform

Further down this same window, find a table with various information from the ID ofsamples in the Affymetrix Probe Set ID, the key genes involved and the mainmetabolic pathways. (the table is too big, then just put key information)
ID Target Description Gene Title Gene Symbol DDR1 RefSeq Transcript ID Gene Ontology Biological Process

1007_s_at

U48705 /FEATURE=mRNA /DEFINITION=HSU48705 Human receptor tyrosine kinase DDR gene, complete cds

discoidin domain receptor tyrosine kinase 1

NM_001954 0006468 // protein amino acid phosphorylation // inferred from /NM_013993 electronic annotation /// 0007155 // cell adhesion // traceable author /NM_013994 statement /// 0007155 // cell adhesion // inferred from electronic annotation /// 0007169 // transmembrane receptor protein tyrosine kinase signaling pathway // inferred from electronic annotation NM_002914 0006260 // DNA replication // not recorded /// 0006260 // DNA /NM_181471 replication // inferred from electronic annotation /// 0006297 // nucleotide-excision repair, DNA gap filling // not recorded NM_002155 0006950 // response to stress // inferred from electronic annotation /// 0006986 // response to unfolded protein // traceable author statement /// 0006986 // response to unfolded protein // non-traceable author

1053_at

M87338 /FEATURE= /DEFINITION=HUMA1SBU Human replication factor C, 40-kDa subunit (A1) mRNA, complete cds X51757 /FEATURE=cds /DEFINITION=HSP70B Human heat-shock protein HSP70B' gene

replication factor C (activator 1) 2, 40kDa heat shock 70kDa protein 6 (HSP70B')

RFC2

117_at

HSPA6

Pgina 2 de Nova Seo 1

/// 0006986 // response to unfolded protein // non-traceable author statement

121_at

X69699 /FEATURE= /DEFINITION=HSPAX8A H.sapiens Pax8 mRNA

paired box 8

PAX8

NM_003466 / NM_013951 / NM_013952 / NM_013953 / NM_013992

0001656 // metanephros development // inferred from electronic annotation /// 0006350 // transcription // inferred from electronic annotation /// 0006355 // regulation of transcription, DNA-dependent // inferred from electronic annotation /// 0007275 // multicellular organismal development // inferred from electronic annotation /// 0009653 // anatomical structure morphogenesis // traceable author statement /// 0030154 // cell differentiation // inferred from electronic annotation /// 0030878 // thyroid gland development // inferred from electronic annotation /// 0045449 // regulation of transcription // inferred from electronic annotation /// 0045893 // positive regulation of transcription, DNA-dependent // inferred from sequence or structural similarity /// 0045944 // positive regulation of transcription from RNA polymerase II promoter // inferred from electronic annotation
0007165 // signal transduction // non-traceable author statement /// 0007601 // visual perception // traceable author statement /// 0007601 // visual perception // inferred from electronic annotation /// 0007602 // phototransduction // inferred from electronic annotation /// 0031282 // regulation of guanylate cyclase activity // inferred from electronic annotation /// 0050896 // response to stimulus // inferred from electronic annotation

1255_g_at

L36861 /FEATURE=expanded_cds /DEFINITION=HUMGCAPB Homo sapiens guanylate cyclase activating protein (GCAP) gene exons 1-4, complete cds

guanylate cyclase activator 1A (retina)

GUCA1A NM_000409

1294_at

L13852 /FEATURE= /DEFINITION=HUME1URP Homo sapiens ubiquitin-activating enzyme E1 related protein mRNA, complete cds

ubiquitin-like modifier activating enzyme 7

UBA7

NM_003335

0006464 // protein modification process // inferred from direct assay /// 0006464 // protein modification process // inferred from electronic annotation /// 0006511 // ubiquitin-dependent protein catabolic process // inferred from electronic annotation /// 0008152 // metabolic process // inferred from electronic annotation /// 0019941 // modification-dependent protein catabolic process // inferred from electronic annotation /// 0032020 // ISG15-protein conjugation // inferred from direct assay /// 0032020 // ISG15-protein conjugation // inferred from electronic annotation

1316_at

X55005 /FEATURE=mRNA /DEFINITION=HSCERBAR thyroid hormone THRA Homo sapiens mRNA for thyroid hormone receptor alpha 1 receptor, alpha THRA1, (c-erbA-1 gene) (erythroblastic leukemia viral (v-erba) oncogene homolog, avian)

NM_003250 0001502 // cartilage condensation // inferred from electronic /NM_199334 annotation /// 0001503 // ossification // inferred from electronic annotation /// 0006350 // transcription // inferred from electronic annotation /// 0006351 // transcription, DNA-dependent // traceable author statement /// 0006355 // regulation of transcription, DNAdependent // inferred from electronic annotation /// 0006366 // transcription from RNA polymerase II promoter // traceable author statement /// 0007623 // circadian rhythm // inferred from electronic annotation /// 0008016 // regulation of heart contraction // inferred from electronic annotation /// 0009887 // organ morphogenesis // inferred from electronic annotation /// 0016481 // negative regulation of transcription // inferred from electronic annotation /// 0043433 // negative regulation of transcription factor activity // inferred from electronic annotation /// 0045944 // positive regulation of transcription from RNA polymerase II promoter // inferred from electronic annotation NM_007039 0006470 // protein amino acid dephosphorylation // traceable author statement /// 0006470 // protein amino acid dephosphorylation // inferred from electronic annotation /// 0016311 // dephosphorylation // inferred from electronic annotation
0006874 // cellular calcium ion homeostasis // traceable author statement /// 0006887 // exocytosis // traceable author statement /// 0006928 // cell motion // traceable author statement /// 0006935 // chemotaxis // traceable author statement /// 0006935 // chemotaxis // inferred from electronic annotation /// 0006954 // inflammatory response // traceable author statement /// 0006954 // inflammatory response // inferred from electronic annotation /// 0006955 // immune response // traceable author statement /// 0006955 // immune response // inferred from electronic annotation /// 0006968 // cellular defense response // traceable author statement /// 0006979 // response to oxidative stress // traceable author statement /// 0007155 // cell adhesion // traceable author statement /// 0007165 // signal transduction // traceable author statement /// 0007267 // cell-cell signaling // traceable author statement /// 0009615 // response to virus // traceable author statement /// 0045071 // negative regulation of viral genome replication // inferred from direct assay 0055114 // oxidation reduction // inferred from electronic annotation

1320_at

X79510 /FEATURE=cds /DEFINITION=HSPTPD1 H.sapiens mRNA for protein-tyrosine-phosphatase D1

protein tyrosine phosphatase, nonreceptor type 21

PTPN21

1405_i_at

M21121 /FEATURE= /DEFINITION=HUMTCSM Human chemokine (C-C T cell-specific protein (RANTES) mRNA, complete cds motif) ligand 5

CCL5

NM_002985

1431_at

J02843 /FEATURE=cds /DEFINITION=HUMCYPIIE Human cytochrome P450IIE1 (ethanol-inducible) gene, complete cds

cytochrome P450, family 2, subfamily E, polypeptide 1

CYP2E1

NM_000773

1438_at

X75208 /FEATURE=cds /DEFINITION=HSPTKR H.sapiens HEK2 mRNA for protein tyrosine kinase receptor

EPH receptor B3

EPHB3

NM_004443

0006468 // protein amino acid phosphorylation // inferred from electronic annotation /// 0007165 // signal transduction // traceable author statement /// 0007169 // transmembrane receptor protein tyrosine kinase signaling pathway // inferred from electronic annotation /// 0007411 // axon guidance // inferred from electronic annotation 0006350 // transcription // inferred from electronic annotation /// 0006355 // regulation of transcription, DNA-dependent // inferred from electronic annotation /// 0045944 // positive regulation of transcription from RNA polymerase II promoter // inferred from electronic annotation 0055114 // oxidation reduction // inferred from electronic annotation

1487_at

L38487 /FEATURE=mRNA /DEFINITION=HUMHERRA1 Human estrogen receptorrelated protein (hERRa1) mRNA, 3' end, partial cds

estrogen-related receptor alpha

ESRRA

NM_004451

1494_f_at

M33318 /FEATURE=mRNA /DEFINITION=HUMCPIIA3A Human cytochrome P450IIA3 (CYP2A3) mRNA, complete cds gb:NM_005505.2 /DB_XREF=gi:21361199 /GEN=SCARB1 /TID=Hs2.180616.1 /CNT=302 /FEA=FLmRNA /TIER=FL+Stack /STK=102 /LL=949 /UG=Hs.180616 /DEF=Homo sapiens scavenger receptor class B, member 1 (SCARB1), mRNA. /PROD=scavenger receptor class B, member 1 /FL=gb:NM_005505.2 gb:NM_015140.1 /DB_XREF=gi:11056035 /TID=Hs2.82563.1 /CNT=210 /FEA=FLmRNA /TIER=FL+Stack /STK=57 /LL=23170 /UG_GENE=KIAA0153 /UG=Hs.82563 /UG_TITLE=KIAA0153 protein /DEF=Homo sapiens Pgina 3 de Nova Seo 1

cytochrome P450, family 2, subfamily A, polypeptide 6 scavenger receptor class B, member 1

CYP2A6

NM_000762

1552256 _a_at

SCARB1

NM_ 001082959 / NM_005505

0006810 // transport // traceable author statement /// 0007155 // cell adhesion // inferred from electronic annotation /// 0008203 // cholesterol metabolic process // traceable author statement /// 0044419 // interspecies interaction between organisms // inferred from electronic annotation 0006464 // protein modification process // inferred from electronic annotation

1552257 _a_at

tubulin tyrosine ligase-like family, member 12

TTLL12

NM_015140

/UG_TITLE=KIAA0153 protein /DEF=Homo sapiens KIAA0153 protein (KIAA0153), mRNA. /FL=gb:NM_ 015140.1 gb:BC001070.1 1552258 _at gb:NM_052871.1 /DB_XREF=gi:16418372 /TID=Hs2.432419.1 /CNT=37 /FEA=FLmRNA /TIER=FL+Stack /STK=25 /LL=112597 /UG_GENE=MGC4677 /UG=Hs.432419 /UG_TITLE=hypothetical protein MGC4677 /DEF=Homo sapiens hypothetical protein MGC4677 (MGC4677), mRNA. /FL=gb:BC010491.1 gb:NM_052871.1 gb:NM_080735.1 /DB_XREF=gi:18379359 /GEN=WFDC2 /TID=Hs2.2719.2 /CNT=26 /FEA=FLmRNA /TIER=FL+Stack /STK=23 /LL=10406 /UG=Hs.2719 /DEF=Homo sapiens WAP four-disulfide core domain 2 (WFDC2), transcript variant 5, mRNA. /PROD=WAP four-disulfide core domain 2, isoform 5 /FL=gb:NM_080735.1 gb:AF330261.1 gb:NM_138957.1 /DB_XREF=gi:20986530 /GEN=MAPK1 /TID=Hs2.324473.2 /CNT=74 /FEA=FLmRNA /TIER=FL+Stack /STK=16 /LL=5594 /UG=Hs.324473 /DEF=Homo sapiens mitogen-activated protein kinase 1 (MAPK1), transcript variant 2, mRNA. /PROD=mitogen-activated protein kinase 1 /FL=gb:NM_ 138957.1 gb:BC017832.1 non-protein coding RNA 152 NCRNA0 NR_024204 / 0152 NR_024205 / NR_024206 / XR_042051 / XR_042052

1552261 _at

WAP four-disulfide core domain 2

WFDC2

NM_006103

0006508 // proteolysis // traceable author statement /// 0007283 // spermatogenesis // traceable author statement

1552263 _at

mitogen-activated protein kinase 1

MAPK1

NM_002745 / 0000165 // MAPKKK cascade // inferred from electronic annotation NM_138957 /// 0006468 // protein amino acid phosphorylation // inferred from electronic annotation /// 0006917 // induction of apoptosis // traceable author statement /// 0006935 // chemotaxis // traceable author statement /// 0006950 // response to stress // traceable author statement /// 0006974 // response to DNA damage stimulus // inferred from electronic annotation /// 0007049 // cell cycle // inferred from electronic annotation /// 0007165 // signal transduction // traceable author statement /// 0007265 // Ras protein signal transduction // not recorded /// 0007268 // synaptic transmission // traceable author statement /// 0009887 // organ morphogenesis // inferred from electronic annotation /// 0019858 // cytosine metabolic process // inferred from electronic annotation /// 0031663 // lipopolysaccharide-mediated signaling pathway // inferred from electronic annotation /// 0032496 // response to lipopolysaccharide // inferred from electronic annotation /// 0043330 // response to exogenous dsRNA // inferred from electronic annotation /// 0044419 // interspecies interaction between organisms // inferred from electronic annotation /// 0045596 // negative regulation of cell differentiation // inferred from electronic annotation /// 0050852 // T cell receptor signaling pathway // inferred from electronic annotation /// 0050853 // B cell receptor signaling pathway // inferred from electronic annotation NM_002745 / 0000165 // MAPKKK cascade // inferred from electronic annotation NM_138957 /// 0006468 // protein amino acid phosphorylation // inferred from electronic annotation /// 0006917 // induction of apoptosis // traceable author statement /// 0006935 // chemotaxis // traceable author statement /// 0006950 // response to stress // traceable author statement /// 0006974 // response to DNA damage stimulus // inferred from electronic annotation /// 0007049 // cell cycle // inferred from electronic annotation /// 0007165 // signal transduction // traceable author statement /// 0007265 // Ras protein signal transduction // not recorded /// 0007268 // synaptic transmission // traceable author statement /// 0009887 // organ morphogenesis // inferred from electronic annotation /// 0019858 // cytosine metabolic process // inferred from electronic annotation /// 0031663 // lipopolysaccharide-mediated signaling pathway // inferred from electronic annotation /// 0032496 // response to lipopolysaccharide // inferred from electronic annotation /// 0043330 // response to exogenous dsRNA // inferred from electronic annotation /// 0044419 // interspecies interaction between organisms // inferred from electronic annotation /// 0045596 // negative regulation of cell differentiation // inferred from electronic annotation /// 0050852 // T cell receptor signaling pathway // inferred from electronic annotation /// 0050853 // B cell receptor signaling pathway // inferred from electronic annotation 0006508 // proteolysis // inferred from electronic annotation /// 0007229 // integrin-mediated signaling pathway // inferred from electronic annotation

1552264 _a_at

gb:NM_138957.1 /DB_XREF=gi:20986530 /GEN=MAPK1 /TID=Hs2.324473.2 /CNT=74 /FEA=FLmRNA /TIER=FL+Stack /STK=16 /LL=5594 /UG=Hs.324473 /DEF=Homo sapiens mitogen-activated protein kinase 1 (MAPK1), transcript variant 2, mRNA. /PROD=mitogen-activated protein kinase 1 /FL=gb:NM_ 138957.1 gb:BC017832.1

mitogen-activated protein kinase 1

MAPK1

1552266 _at

gb:NM_145004.1 /DB_XREF=gi:21450712 /TID=Hs2.338203.1 /CNT=38 /FEA=FLmRNA /TIER=FL+Stack /STK=15 /LL=203102 /UG_GENE=MGC26899 /UG=Hs.338203 /UG_TITLE=hypothetical protein MGC26899 /DEF=Homo sapiens a disintegrin and metalloprotease domain 32 (ADAM32), mRNA. /FL=gb:BC030698.1 gb:NM_145004.1 gb:BC030014.1 gb:BC026085.1 gb:BC028702.1 gb:BC026169.1 gb:BC034975.1

ADAM metallopeptidase domain 32

ADAM32 NM_145004

Then we went to check out the article and the information and details about the study

Pgina 4 de Nova Seo 1

Then we went to check out the article and the information and details about the study

2 - Perform cluster analysis. Enlist 20 significantly overexpressed genes differentiating the two groups and provide some information on how to obtain genes that are in the same chromosome or have identical/similar expression profiles (examples for 5 genes that were initially selected). Obtained basic information about the study in question, we begin the process ofcluster analysis. Even in the information window on the dataset entered the Geo tabCompare two sets of samples and in Step 2 separate samples by disease status, and the normal group A and group B those affected. And finally clicked in Step 3: Group A vs. Query. B leads to a new window.

In the new window that opened several genes appear and clicking on ProfileNeighbors to filter them as similar profiles

Pgina 5 de Nova Seo 1

them as similar profiles

After you click Profile Neighbors in the gene and then DCAF15 ChromosomeNeighbors had the following result:
Results: 20 1: GDS1989 record | GPL570 91952_at [Homo sapiens] 18 samples Profile Neighbors, Chromosome Neighbors, Homologs, Links
Annotation: DCAF15: DDB1 and CUL4 associated factor 15 C19orf72, MGC99481

Reporter:

AI363375

Experiment: Melanoma progression, Expression profiling by array, count

2: GDS1989 record | GPL570 222012_at [Homo sapiens] 18 samples Profile Neighbors, Chromosome Neighbors, Homologs, Links Annotation: Reporter: DCAF15: DDB1 and CUL4 associated factor 15 C19orf72, MGC99481 AA535066

Experiment: Melanoma progression, Expression profiling by array, count

3: GDS1989 record | GPL570 221851_at [Homo sapiens] 18 samples Profile Neighbors, Chromosome Neighbors, Homologs, Links Annotation: Reporter: DCAF15: DDB1 and CUL4 associated factor 15 C19orf72, MGC99481 AI073983

Experiment: Melanoma progression, Expression profiling by array, count

4: GDS1989 record | GPL570 221849_s_at [Homo sapiens] 18 samples Profile Neighbors, Chromosome Neighbors, Homologs, Links

Annotation: Reporter:

DCAF15: DDB1 and CUL4 associated factor 15 C19orf72, MGC99481 AA733079

Experiment: Melanoma progression, Expression profiling by array, count

Pgina 6 de Nova Seo 1

5: GDS1989 record | GPL570 220411_x_at [Homo sapiens] Annotation: Reporter: PODNL1: podocan-like 1 FLJ23447, SLRR5B NM_024825

18 samples Profile Neighbors, Chromosome Neighbors, Sequence Neighbors, Homologs,Links

Experiment: Melanoma progression, Expression profiling by array, count

6: GDS1989 record | GPL570 226786_at [Homo sapiens] 18 samples Profile Neighbors, Chromosome Neighbors, Homologs, Links Annotation: Reporter: RFX1: regulatory factor X, 1 (influences HLA class II expression) EFC, RFX BF507952

Experiment: Melanoma progression, Expression profiling by array, count

7: GDS1989 record | GPL570 206321_at [Homo sapiens] Annotation: Reporter:

18 samples Profile Neighbors, Chromosome Neighbors, Sequence Neighbors, Homologs, Links

RFX1: regulatory factor X, 1 (influences HLA class II expression) EFC, RFX NM_002918

Experiment: Melanoma progression, Expression profiling by array, count

8: GDS1989 record | GPL570 58994_at [Homo sapiens] 18 samples Profile Neighbors, Chromosome Neighbors, Homologs, Links Annotation: CC2D1A: coiled-coil and C2 domain containing 1A FLJ20241, FLJ41160, FREUD-1, Freud-1/Aki1, MRT3

Reporter:

AI689402

Experiment: Melanoma progression, Expression profiling by array, count

9: GDS1989 record | GPL570 222137_at [Homo sapiens]

18 samples Profile Neighbors, Chromosome Neighbors, Sequence Neighbors, Homologs, Links

Annotation: CC2D1A: coiled-coil and C2 domain containing 1A FLJ20241, FLJ41160, FREUD-1, Freud-1/Aki1, MRT3

Reporter:

AK023399

Experiment: Melanoma progression, Expression profiling by array, count 10: GDS1989 record | GPL570 221888_at [Homo sapiens] 18 samples Profile Neighbors, Chromosome Neighbors, Homologs, Links Annotation: CC2D1A: coiled-coil and C2 domain containing 1A FLJ20241, FLJ41160, FREUD-1, Freud-1/Aki1, MRT3

Reporter:

AW183030

Experiment: Melanoma progression, Expression profiling by array, count

11: GDS1989 record | GPL570 207083_s_at [Homo sapiens]

18 samples Profile Neighbors, Chromosome Neighbors, Sequence Neighbors, Homologs,Links

Annotation: CC2D1A: coiled-coil and C2 domain containing 1A FLJ20241, FLJ41160, FREUD-1,

Pgina 7 de Nova Seo 1

11: GDS1989 record | GPL570 207083_s_at [Homo sapiens]

18 samples Profile Neighbors, Chromosome Neighbors, Sequence Neighbors, Homologs,Links

Annotation: CC2D1A: coiled-coil and C2 domain containing 1A FLJ20241, FLJ41160, FREUD-1, Freud-1/Aki1, MRT3

Reporter:

NM_017721

Experiment Melanoma progression, Expression profiling by array, count :

12: GDS1989 record | GPL570 206901_at [Homo sapiens] Annotation: Reporter:

18 samples Profile Neighbors, Chromosome Neighbors, Sequence Neighbors, Homologs,Links

C19orf57: chromosome 19 open reading frame 57 MGC11271, MGC149720 NM_024323

Experiment: Melanoma progression, Expression profiling by array, count

13: GDS1989 record | GPL570 1553403_at [Homo sapiens] Annotation: Reporter:

18 samples Profile Neighbors, Chromosome Neighbors, Sequence Neighbors, Homologs,Links

RLN3: relaxin 3 UNQ6188/PRO20213, H3, RXN3, ZINS4, insl7 AB076563

Experiment: Melanoma progression, Expression profiling by array, count

14: GDS1989 record | GPL570 240311_at [Homo sapiens] 18 samples Profile Neighbors, Chromosome Neighbors, Homologs, Links

Annotation: Reporter:

NANOS3: nanos homolog 3 (Drosophila) MGC120114, NANOS1L, NOS3 AI801869

Experiment: Melanoma progression, Expression profiling by array, count 15: GDS1989 record | GPL570 222062_at [Homo sapiens] 18 samples Profile Neighbors, Chromosome Neighbors, Homologs, Links Annotation: IL27RA: interleukin 27 receptor, alpha UNQ296/PRO336, CRL1, IL27R, TCCR, WSX1, zcytor1

Reporter:

AI983115

Experiment: Melanoma progression, Expression profiling by array, count 16: GDS1989 record | GPL570 217702_at [Homo sapiens] 18 samples Profile Neighbors, Chromosome Neighbors, Homologs, Links Annotation: IL27RA: interleukin 27 receptor, alpha UNQ296/PRO336, CRL1, IL27R, TCCR, WSX1, zcytor1

Reporter:

AW295066

Experiment: Melanoma progression, Expression profiling by array, count

17: GDS1989 record | GPL570 205926_at [Homo sapiens] Annotation: Reporter:

18 samples Profile Neighbors, Chromosome Neighbors, Sequence Neighbors, Homologs,Links

IL27RA: interleukin 27 receptor, alpha UNQ296/PRO336, CRL1, IL27R, TCCR, WSX1, zcytor1 NM_004843

Experiment: Melanoma progression, Expression profiling by array, count

Pgina 8 de Nova Seo 1

Annotation:
Reporter:

PALM3: paralemmin 3
BF195936

Experiment: Melanoma progression, Expression profiling by array, count

19: GDS1989 record | GPL570 1558412_at [Homo sapiens] Annotation: Reporter: LOC113230: hypothetical protein LOC113230 BC011002

18 samples Profile Neighbors, Chromosome Neighbors, Sequence Neighbors, Links

Experiment: Melanoma progression, Expression profiling by array, count

20: GDS1989 record | GPL570 225650_at [Homo sapiens] 18 samples Profile Neighbors, Chromosome Neighbors, Homologs, Links
Annotation: SAMD1: sterile alpha motif domain containing 1

Reporter:

BF207100

Experiment: Melanoma progression, Expression profiling by array, count

Back to GEODataSet information. Tab of Data Analysis Tools Cluster Heatmaps and clicking Display opens a new window with the formation of the cluster according toour analysis in the previous step

In the new window, open a new cluster formed from the new analysis we made ofgroups of samples Compare the two sets of samples.

Pgina 9 de Nova Seo 1

samples Compare the two sets of samples.

3 - What was the number of major affected pathways? Provide a list of 10 most significant pathways differentiating the two groups with their source. After finding the 20 genes with similar overexpression we click on Find Patway on the right side of the window to find the metabolic pathways and related genes.

Pgina 10 de Nova Seo 1

pathways differentiating the two groups with their source. After finding the 20 genes with similar overexpression we click on Find Patway on the right side of the window to find the metabolic pathways and related genes.

10 routes found

Pgina 11 de Nova Seo 1

4 - How GeneMANIA or AmiGO can help you define potential biomarkers? Can you provide the network created by GeneMANIA for all the 20 genes selected in the previous question? Through GeneMANIA or AmiGO we can find: new members of a pathway or complex Identify additional genes missed in screens Classify new members of a functional class of proteins The GeneMANIA algorithm performs as well or better than other gene function prediction methods on yeast and mouse benchmarks. The high accuracy of the GeneMANIA prediction algorithm, an intuitive user interface and large database make GeneMANIA a useful tool for any biologist. GeneMANIA: Related Genes: DCAF15; CC2D1A; IL27RA; RFX1; PALM3; NANOS3; RLN3; LOC113230; SAMD1; PODNL1 Network of 10 related genes found:

Pgina 12 de Nova Seo 1

Network of 10 related genes found:

Pgina 13 de Nova Seo 1