Scientific

MK5 Microarray Data

Affected Genes - Ontology Breakdown - Gene Enrichment - Proteome Analysis

These are the micro-array results of a differential gene expression microarray experiments and the subsequent analysis steps performed on them. The up/down- regulation ratio was obtained by measuring WT cells against MK5 activated cells. See material and methods for technical information as well as the data usage policy.

MK5 Proteome Analysis

Table 3: Type II network, divided ranks. This table presents the output of the simulation of a type-II network in which we relied on the high confidence interactions and micro-array results. The output of the micro-array was then ranked and these ranks used as input into the network simulation. After performing two such simulations (one for the MK5 off and one for the MK5 on microarray output), we divided the ranks and sorted the results accordingly. The output of this technique is a collection of proteins that cluster naturally together.


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Rank Gene Hugo description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 3012 to 3061 of 6456 in total
Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1
Rank
Hugo
description
Network Comparison Type
red
green
network_comparison
1506 FAT cadherin-related tumor suppressor homolog precursor (fat protein homolog). [swissprot;acc:q14517] Subtracted 219.306 223.179 3.873
1507 PDK1 [pyruvate dehydrogenase [lipoamide]] kinase isozyme 1, mitochondrial precursor (ec 2.7.1.99) (pyruvate dehydrogenase kinase isoform 1). [swissprot;acc:q15118] Divided 213.274 209.5 1.01801
STARD3NL mln64 n-terminal domain homolog (stard3 n-terminal like protein). [swissprot;acc:o95772] Subtracted 219.306 223.179 3.873
1508 CPSF3 cleavage and polyadenylation specificity factor, 73 kda subunit (cpsf 73 kda subunit). [swissprot;acc:q9ukf6] 116.524 120.375 3.851
PDK2 [pyruvate dehydrogenase [lipoamide]] kinase isozyme 2, mitochondrial precursor (ec 2.7.1.99) (pyruvate dehydrogenase kinase isoform 2). [swissprot;acc:q15119] Divided 213.274 209.5 1.01801
1509 ACTR1A alpha-centractin (centractin) (centrosome-associated actin homolog) (actin-rpv) (arp1). [swissprot;acc:p42024] 225.148 221.177 1.01795
PDHA2 pyruvate dehydrogenase e1 component alpha subunit, testis-specific form, mitochondrial precursor (ec 1.2.4.1) (pdhe1-a type ii). [swissprot;acc:p29803] Subtracted 204.146 207.988 3.842
1510 ACTR1B beta-centractin (actin-related protein 1b) (arp1b). [swissprot;acc:p42025] Divided 225.148 221.177 1.01795
CCDC53 protein ad-016 (protein cgi-116) (x0009). [swissprot;acc:q9y3c0] Subtracted 216.158 212.316 3.842
1511 COX11 cytochrome c oxidase assembly protein cox11, mitochondrial precursor. [swissprot;acc:q9y6n1] Divided 213.268 209.509 1.01794
PDHA1 pyruvate dehydrogenase e1 component alpha subunit, somatic form, mitochondrial precursor (ec 1.2.4.1) (pdhe1-a type i). [swissprot;acc:p08559] Subtracted 204.133 207.967 3.834
1512 ECHS1 enoyl-coa hydratase, mitochondrial precursor (ec 4.2.1.17) (short chain enoyl-coa hydratase) (sceh) (enoyl-coa hydratase 1). [swissprot;acc:p30084] 184.656 180.823 3.833
SURF1 surfeit locus protein 1. [swissprot;acc:q15526] Divided 213.268 209.509 1.01794
1513 COX15 cox15 homolog isoform 2 precursor; cytochrome c oxidase subunit 15; cytochrome c oxidase assembly protein. [refseq;acc:nm_004376]
DUT deoxyuridine 5'-triphosphate nucleotidohydrolase, mitochondrial precursor (ec 3.6.1.23) (dutpase) (dutp pyrophosphatase). [swissprot;acc:p33316] Subtracted 187.114 190.925 3.811
1514 COX10 protoheme ix farnesyltransferase, mitochondrial precursor (ec 2.5.1.-) (heme o synthase). [swissprot;acc:q12887] Divided 213.268 209.509 1.01794
PDHB pyruvate dehydrogenase e1 component beta subunit, mitochondrial precursor (ec 1.2.4.1) (pdhe1-b). [swissprot;acc:p11177] Subtracted 198.927 202.726 3.799
1515 DPP10 dipeptidylpeptidase 10; dipeptidyl peptidase iv-related protein 3. [refseq;acc:nm_020868] Divided 213.267 209.511 1.01793
TMEM91 2-oxoisovalerate dehydrogenase alpha subunit, mitochondrial precursor (ec 1.2.4.4) (branched-chain alpha-keto acid dehydrogenase e1 component alpha chain) (bckdh e1-alpha). [swissprot;acc:p12694] Subtracted 198.927 202.726 3.799
1516 DPP6 dipeptidyl aminopeptidase-like protein 6 (dipeptidylpeptidase vi) (dipeptidylpeptidase 6) (dipeptidyl peptidase iv like protein) (dipeptidyl aminopeptidase-related protein) (dppx). [swissprot;acc:p42658] Divided 213.267 209.511 1.01793
POLE2 dna polymerase epsilon subunit b (ec 2.7.7.7) (dna polymerase ii subunit b). [swissprot;acc:p56282] Subtracted 246.38 242.596 3.784
1517 FAP seprase (ec 3.4.21.-) (fibroblast activation protein alpha) (integral membrane serine protease) (170-kda melanoma membrane-bound gelatinase). [swissprot;acc:q12884] Divided 213.267 209.511 1.01793
PDK1 [pyruvate dehydrogenase [lipoamide]] kinase isozyme 1, mitochondrial precursor (ec 2.7.1.99) (pyruvate dehydrogenase kinase isoform 1). [swissprot;acc:q15118] Subtracted 213.274 209.5 3.774
1518 BCKDK [3-methyl-2-oxobutanoate dehydrogenase [lipoamide]] kinase, mitochondrial precursor (ec 2.7.1.115) (branched-chain alpha-ketoacid dehydrogenase kinase) (bckdhkin) (bckd-kinase). [swissprot;acc:o14874] Divided 213.259 209.524 1.01783
PDK2 [pyruvate dehydrogenase [lipoamide]] kinase isozyme 2, mitochondrial precursor (ec 2.7.1.99) (pyruvate dehydrogenase kinase isoform 2). [swissprot;acc:q15119] Subtracted 213.274 209.5 3.774
1519 CRX cone-rod homeobox protein. [swissprot;acc:o43186] Divided 244.331 240.061 1.01779
FOXA3 hepatocyte nuclear factor 3-gamma (hnf-3g) (forkhead box protein a3) (fork head-related protein fkh h3). [swissprot;acc:p55318] Subtracted 217.785 214.021 3.764
1520 C16orf42 c316g12.2 (novel protein similar to predicted yeast, worm and archae- bacterial proteins) (similar to und313) (s. cervisiae) (hypothetical protein). [sptrembl;acc:q9ujk0] 212.103 208.339
OTX1 homeobox protein otx1. [swissprot;acc:p32242] Divided 244.367 240.098 1.01778
1521 COX11 cytochrome c oxidase assembly protein cox11, mitochondrial precursor. [swissprot;acc:q9y6n1] Subtracted 213.268 209.509 3.759
OTX2 homeobox protein otx2. [swissprot;acc:p32243] Divided 244.478 240.212 1.01776
1522 MPI mannose-6-phosphate isomerase (ec 5.3.1.8) (phosphomannose isomerase) (pmi) (phosphohexomutase). [swissprot;acc:p34949] 219.306 223.179 1.01766
SURF1 surfeit locus protein 1. [swissprot;acc:q15526] Subtracted 213.268 209.509 3.759
1523 no value putative ankyrin-repeat containing protein. [refseq;acc:nm_025185] Divided 219.306 223.179 1.01766
COX15 cox15 homolog isoform 2 precursor; cytochrome c oxidase subunit 15; cytochrome c oxidase assembly protein. [refseq;acc:nm_004376] Subtracted 213.268 209.509 3.759
1524 COX10 protoheme ix farnesyltransferase, mitochondrial precursor (ec 2.5.1.-) (heme o synthase). [swissprot;acc:q12887]
STARD3 mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849] Divided 219.306 223.179 1.01766
1525 DPP10 dipeptidylpeptidase 10; dipeptidyl peptidase iv-related protein 3. [refseq;acc:nm_020868] Subtracted 213.267 209.511 3.756
FAT2 protocadherin fat 2 precursor (hfat2) (multiple epidermal growth factor-like domains 1). [swissprot;acc:q9nyq8] Divided 219.306 223.179 1.01766
1526 DPP6 dipeptidyl aminopeptidase-like protein 6 (dipeptidylpeptidase vi) (dipeptidylpeptidase 6) (dipeptidyl peptidase iv like protein) (dipeptidyl aminopeptidase-related protein) (dppx). [swissprot;acc:p42658] Subtracted 213.267 209.511 3.756
FAT cadherin-related tumor suppressor homolog precursor (fat protein homolog). [swissprot;acc:q14517] Divided 219.306 223.179 1.01766
1527 FAP seprase (ec 3.4.21.-) (fibroblast activation protein alpha) (integral membrane serine protease) (170-kda melanoma membrane-bound gelatinase). [swissprot;acc:q12884] Subtracted 213.267 209.511 3.756
STARD3NL mln64 n-terminal domain homolog (stard3 n-terminal like protein). [swissprot;acc:o95772] Divided 219.306 223.179 1.01766
1528 FOXA3 hepatocyte nuclear factor 3-gamma (hnf-3g) (forkhead box protein a3) (fork head-related protein fkh h3). [swissprot;acc:p55318] 217.785 214.021 1.01759
MLLT4 af-6 protein. [swissprot;acc:p55196] Subtracted 218.733 214.98 3.753
1529 ACTG1 actin, cytoplasmic 2 (gamma-actin). [swissprot;acc:p02571] Divided 216.762 213.031 1.01751
MYB myb proto-oncogene protein (c-myb). [swissprot;acc:p10242] Subtracted 222.672 218.92 3.752
1530 CDC25B m-phase inducer phosphatase 2 (ec 3.1.3.48) (dual specificity phosphatase cdc25b). [swissprot;acc:p30305] 260.269 256.531 3.738
MLLT4 af-6 protein. [swissprot;acc:p55196] Divided 218.733 214.98 1.01746
1531 CRIM1 cysteine-rich motor neuron 1; cysteine-rich repeat-containing protein s52 precursor. [refseq;acc:nm_016441] 217.025 213.304 1.01744

Legend:
- Rank is the rank after comparing the two networks
- Gene is the ensembl human gene identifier measured by 1 or more probes on the microarray
- Hugo is the HGNC identifier if it exists
- Value Type describes how the microarray measurement was processed. Ranked indicates that we sorted all measurements and use the rank as red and green value. Measured is the normal measurement. Squared and Rooted are the square and square root respecitcely. This might be valueable to compensate for non linear light distributions.
- Network Comparison Type describes whether we divided the red and green types or whether we sutractcted them
- Interaction Map specifies whether we used only the hig hconfidence protein-protein interactions or also included the low confidence interactions.
- Filtered specifies whether we only included the high confidence microarry measurements or not.
- http://analysis.yellowcouch.org/