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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Gene Rank description Network Comparison Type Value Type Interaction Map Filtered green red 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
description
Network Comparison Type
green
red
network_comparison
1506 cadherin-related tumor suppressor homolog precursor (fat protein homolog). [swissprot;acc:q14517] Subtracted 223.179 219.306 3.873
1507 mln64 n-terminal domain homolog (stard3 n-terminal like protein). [swissprot;acc:o95772]
[pyruvate dehydrogenase [lipoamide]] kinase isozyme 1, mitochondrial precursor (ec 2.7.1.99) (pyruvate dehydrogenase kinase isoform 1). [swissprot;acc:q15118] Divided 209.5 213.274 1.01801
1508 cleavage and polyadenylation specificity factor, 73 kda subunit (cpsf 73 kda subunit). [swissprot;acc:q9ukf6] Subtracted 120.375 116.524 3.851
[pyruvate dehydrogenase [lipoamide]] kinase isozyme 2, mitochondrial precursor (ec 2.7.1.99) (pyruvate dehydrogenase kinase isoform 2). [swissprot;acc:q15119] Divided 209.5 213.274 1.01801
1509 alpha-centractin (centractin) (centrosome-associated actin homolog) (actin-rpv) (arp1). [swissprot;acc:p42024] 221.177 225.148 1.01795
pyruvate dehydrogenase e1 component alpha subunit, testis-specific form, mitochondrial precursor (ec 1.2.4.1) (pdhe1-a type ii). [swissprot;acc:p29803] Subtracted 207.988 204.146 3.842
1510 beta-centractin (actin-related protein 1b) (arp1b). [swissprot;acc:p42025] Divided 221.177 225.148 1.01795
protein ad-016 (protein cgi-116) (x0009). [swissprot;acc:q9y3c0] Subtracted 212.316 216.158 3.842
1511 cytochrome c oxidase assembly protein cox11, mitochondrial precursor. [swissprot;acc:q9y6n1] Divided 209.509 213.268 1.01794
pyruvate dehydrogenase e1 component alpha subunit, somatic form, mitochondrial precursor (ec 1.2.4.1) (pdhe1-a type i). [swissprot;acc:p08559] Subtracted 207.967 204.133 3.834
1512 enoyl-coa hydratase, mitochondrial precursor (ec 4.2.1.17) (short chain enoyl-coa hydratase) (sceh) (enoyl-coa hydratase 1). [swissprot;acc:p30084] 180.823 184.656 3.833
surfeit locus protein 1. [swissprot;acc:q15526] Divided 209.509 213.268 1.01794
1513 cox15 homolog isoform 2 precursor; cytochrome c oxidase subunit 15; cytochrome c oxidase assembly protein. [refseq;acc:nm_004376]
deoxyuridine 5'-triphosphate nucleotidohydrolase, mitochondrial precursor (ec 3.6.1.23) (dutpase) (dutp pyrophosphatase). [swissprot;acc:p33316] Subtracted 190.925 187.114 3.811
1514 protoheme ix farnesyltransferase, mitochondrial precursor (ec 2.5.1.-) (heme o synthase). [swissprot;acc:q12887] Divided 209.509 213.268 1.01794
pyruvate dehydrogenase e1 component beta subunit, mitochondrial precursor (ec 1.2.4.1) (pdhe1-b). [swissprot;acc:p11177] Subtracted 202.726 198.927 3.799
1515 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]
dipeptidylpeptidase 10; dipeptidyl peptidase iv-related protein 3. [refseq;acc:nm_020868] Divided 209.511 213.267 1.01793
1516 dipeptidyl aminopeptidase-like protein 6 (dipeptidylpeptidase vi) (dipeptidylpeptidase 6) (dipeptidyl peptidase iv like protein) (dipeptidyl aminopeptidase-related protein) (dppx). [swissprot;acc:p42658]
dna polymerase epsilon subunit b (ec 2.7.7.7) (dna polymerase ii subunit b). [swissprot;acc:p56282] Subtracted 242.596 246.38 3.784
1517 seprase (ec 3.4.21.-) (fibroblast activation protein alpha) (integral membrane serine protease) (170-kda melanoma membrane-bound gelatinase). [swissprot;acc:q12884] Divided 209.511 213.267 1.01793
[pyruvate dehydrogenase [lipoamide]] kinase isozyme 1, mitochondrial precursor (ec 2.7.1.99) (pyruvate dehydrogenase kinase isoform 1). [swissprot;acc:q15118] Subtracted 209.5 213.274 3.774
1518 [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 209.524 213.259 1.01783
[pyruvate dehydrogenase [lipoamide]] kinase isozyme 2, mitochondrial precursor (ec 2.7.1.99) (pyruvate dehydrogenase kinase isoform 2). [swissprot;acc:q15119] Subtracted 209.5 213.274 3.774
1519 cone-rod homeobox protein. [swissprot;acc:o43186] Divided 240.061 244.331 1.01779
hepatocyte nuclear factor 3-gamma (hnf-3g) (forkhead box protein a3) (fork head-related protein fkh h3). [swissprot;acc:p55318] Subtracted 214.021 217.785 3.764
1520 c316g12.2 (novel protein similar to predicted yeast, worm and archae- bacterial proteins) (similar to und313) (s. cervisiae) (hypothetical protein). [sptrembl;acc:q9ujk0] 208.339 212.103
homeobox protein otx1. [swissprot;acc:p32242] Divided 240.098 244.367 1.01778
1521 cytochrome c oxidase assembly protein cox11, mitochondrial precursor. [swissprot;acc:q9y6n1] Subtracted 209.509 213.268 3.759
homeobox protein otx2. [swissprot;acc:p32243] Divided 240.212 244.478 1.01776
1522 mannose-6-phosphate isomerase (ec 5.3.1.8) (phosphomannose isomerase) (pmi) (phosphohexomutase). [swissprot;acc:p34949] 223.179 219.306 1.01766
surfeit locus protein 1. [swissprot;acc:q15526] Subtracted 209.509 213.268 3.759
1523 cox15 homolog isoform 2 precursor; cytochrome c oxidase subunit 15; cytochrome c oxidase assembly protein. [refseq;acc:nm_004376]
putative ankyrin-repeat containing protein. [refseq;acc:nm_025185] Divided 223.179 219.306 1.01766
1524 mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849]
protoheme ix farnesyltransferase, mitochondrial precursor (ec 2.5.1.-) (heme o synthase). [swissprot;acc:q12887] Subtracted 209.509 213.268 3.759
1525 dipeptidylpeptidase 10; dipeptidyl peptidase iv-related protein 3. [refseq;acc:nm_020868] 209.511 213.267 3.756
protocadherin fat 2 precursor (hfat2) (multiple epidermal growth factor-like domains 1). [swissprot;acc:q9nyq8] Divided 223.179 219.306 1.01766
1526 cadherin-related tumor suppressor homolog precursor (fat protein homolog). [swissprot;acc:q14517]
dipeptidyl aminopeptidase-like protein 6 (dipeptidylpeptidase vi) (dipeptidylpeptidase 6) (dipeptidyl peptidase iv like protein) (dipeptidyl aminopeptidase-related protein) (dppx). [swissprot;acc:p42658] Subtracted 209.511 213.267 3.756
1527 mln64 n-terminal domain homolog (stard3 n-terminal like protein). [swissprot;acc:o95772] Divided 223.179 219.306 1.01766
seprase (ec 3.4.21.-) (fibroblast activation protein alpha) (integral membrane serine protease) (170-kda melanoma membrane-bound gelatinase). [swissprot;acc:q12884] Subtracted 209.511 213.267 3.756
1528 af-6 protein. [swissprot;acc:p55196] 214.98 218.733 3.753
hepatocyte nuclear factor 3-gamma (hnf-3g) (forkhead box protein a3) (fork head-related protein fkh h3). [swissprot;acc:p55318] Divided 214.021 217.785 1.01759
1529 actin, cytoplasmic 2 (gamma-actin). [swissprot;acc:p02571] 213.031 216.762 1.01751
myb proto-oncogene protein (c-myb). [swissprot;acc:p10242] Subtracted 218.92 222.672 3.752
1530 af-6 protein. [swissprot;acc:p55196] Divided 214.98 218.733 1.01746
m-phase inducer phosphatase 2 (ec 3.1.3.48) (dual specificity phosphatase cdc25b). [swissprot;acc:p30305] Subtracted 256.531 260.269 3.738
1531 cysteine-rich motor neuron 1; cysteine-rich repeat-containing protein s52 precursor. [refseq;acc:nm_016441] Divided 213.304 217.025 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
- 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/