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 - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.


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Rank Gene description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 2813 to 2862 of 6456 in total
Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
red
green
network_comparison
1407 wd repeat and fyve domain containing 1 isoform 1; phosphoinositide-binding protein sr1; wd40 and fyve domain containing 1. [refseq;acc:nm_020830] Divided 206.104 210.424 1.02096
Subtracted 4.32
1408 stromal interaction molecule 1 precursor. [swissprot;acc:q13586] Divided 206.102 210.42 1.02095
Subtracted 4.318
1409 trap/mediator complex component trap25. [refseq;acc:nm_080651] Divided 1.02095
Subtracted 4.318
1410 serine/threonine-protein kinase pak 4 (ec 2.7.1.-) (p21-activated kinase 4) (pak-4). [swissprot;acc:o96013]
wd repeat- and fyve domain-containing protein 2; wd40 and fyve domain containing 2. [refseq;acc:nm_052950] Divided 206.1 210.417 1.02095
1411 polyposis locus protein 1 (tb2 protein). [swissprot;acc:q00765] Subtracted 206.102 210.42 4.318
serine/threonine-protein kinase pak 4 (ec 2.7.1.-) (p21-activated kinase 4) (pak-4). [swissprot;acc:o96013] Divided 1.02095
1412 acyl-coa dehydrogenase, medium-chain specific, mitochondrial precursor (ec 1.3.99.3) (mcad). [swissprot;acc:p11310] Subtracted 4.318
polyposis locus protein 1 (tb2 protein). [swissprot;acc:q00765] Divided 1.02095
1413 acyl-coa dehydrogenase, medium-chain specific, mitochondrial precursor (ec 1.3.99.3) (mcad). [swissprot;acc:p11310]
polyposis locus protein 1-like 1; likely ortholog of mouse polyposis locus protein 1-like 1. [refseq;acc:nm_138393] Subtracted 4.318
1414 Divided 1.02095
stromal interaction molecule 2 precursor. [swissprot;acc:q9p246] Subtracted 4.318
1415 serine/threonine-protein kinase pak 7 (ec 2.7.1.-) (p21-activated kinase 7) (pak-7) (pak-5). [swissprot;acc:q9p286]
stromal interaction molecule 2 precursor. [swissprot;acc:q9p246] Divided 1.02095
1416 serine/threonine-protein kinase pak 7 (ec 2.7.1.-) (p21-activated kinase 7) (pak-7) (pak-5). [swissprot;acc:q9p286]
wd repeat- and fyve domain-containing protein 2; wd40 and fyve domain containing 2. [refseq;acc:nm_052950] Subtracted 206.1 210.417 4.317
1417 acid ceramidase precursor (ec 3.5.1.23) (acylsphingosine deacylase) (n-acylsphingosine amidohydrolase) (ac) (putative 32 kda heart protein) (php32). [swissprot;acc:q13510] 207.076 211.391 4.315
carboxypeptidase a5. [refseq;acc:nm_080385] Divided 203.979 208.229 1.02084
1418 carboxypeptidase b precursor (ec 3.4.17.2) (pancreas-specific protein) (pasp). [swissprot;acc:p15086]
cone-rod homeobox protein. [swissprot;acc:o43186] Subtracted 244.331 240.061 4.27
1419 homeobox protein otx1. [swissprot;acc:p32242] 244.367 240.098 4.269
neutral and basic amino acid transport protein rbat (b(0,+)-type amino acid transport protein) (nbat) (d2h). [swissprot;acc:q07837] Divided 203.979 208.229 1.02084
1420 aminoacylase-1 (ec 3.5.1.14) (n-acyl-l-amino-acid amidohydrolase) (acy-1). [swissprot;acc:q03154]
homeobox protein otx2. [swissprot;acc:p32243] Subtracted 244.478 240.212 4.266
1421 acid ceramidase precursor (ec 3.5.1.23) (acylsphingosine deacylase) (n-acylsphingosine amidohydrolase) (ac) (putative 32 kda heart protein) (php32). [swissprot;acc:q13510] Divided 207.076 211.391 1.02084
carboxypeptidase a5. [refseq;acc:nm_080385] Subtracted 203.979 208.229 4.25
1422 carboxypeptidase a1 precursor (ec 3.4.17.1). [swissprot;acc:p15085] Divided 1.02084
carboxypeptidase b precursor (ec 3.4.17.2) (pancreas-specific protein) (pasp). [swissprot;acc:p15086] Subtracted 4.25
1423 cysteine-rich protein 1 (cysteine-rich intestinal protein) (crip) (cysteine-rich heart protein) (hcrhp). [swissprot;acc:p50238] Divided 221.152 216.659 1.02074
neutral and basic amino acid transport protein rbat (b(0,+)-type amino acid transport protein) (nbat) (d2h). [swissprot;acc:q07837] Subtracted 203.979 208.229 4.25
1424 aminoacylase-1 (ec 3.5.1.14) (n-acyl-l-amino-acid amidohydrolase) (acy-1). [swissprot;acc:q03154]
sodium/potassium-transporting atpase alpha-1 chain precursor (ec 3.6.3.9) (sodium pump 1) (na+/k+ atpase 1). [swissprot;acc:p05023] Divided 214.717 219.157 1.02068
1425 carboxypeptidase a1 precursor (ec 3.4.17.1). [swissprot;acc:p15085] Subtracted 203.979 208.229 4.25
cathepsin l2 precursor (ec 3.4.22.43) (cathepsin v) (cathepsin u). [swissprot;acc:o60911] Divided 214.717 219.157 1.02068
1426 cathepsin l precursor (ec 3.4.22.15) (major excreted protein) (mep). [swissprot;acc:p07711]
protein cgi-147. [swissprot;acc:q9y3e5] Subtracted 221.961 226.186 4.225
1427 casein kinase i alpha s-like. [refseq;acc:nm_145203] 229.459 225.237 4.222
sodium/potassium-transporting atpase alpha-3 chain (ec 3.6.3.9) (sodium pump 3) (na+/k+ atpase 3) (alpha(iii)). [swissprot;acc:p13637] Divided 214.717 219.157 1.02068
1428 casein kinase i, alpha isoform (ec 2.7.1.-) (cki-alpha) (ck1). [swissprot;acc:p48729] Subtracted 229.459 225.237 4.222
sodium/potassium-transporting atpase alpha-2 chain precursor (ec 3.6.3.9) (sodium pump 2) (na+/k+ atpase 2). [swissprot;acc:p50993] Divided 214.717 219.157 1.02068
1429 glutaminyl-trna synthetase (ec 6.1.1.18) (glutamine--trna ligase) (glnrs). [swissprot;acc:p47897] Subtracted 221.412 217.199 4.213
wd repeat domain 26. [refseq;acc:nm_025160] Divided 213.351 217.74 1.02057
1430 deoxyuridine 5'-triphosphate nucleotidohydrolase, mitochondrial precursor (ec 3.6.1.23) (dutpase) (dutp pyrophosphatase). [swissprot;acc:p33316] 187.114 190.925 1.02037
spermidine synthase (ec 2.5.1.16) (putrescine aminopropyltransferase) (spdsy). [swissprot;acc:p19623] Subtracted 221.412 217.199 4.213
1431 glycyl-trna synthetase (ec 6.1.1.14) (glycine--trna ligase) (glyrs). [swissprot;acc:p41250]
uv excision repair protein rad23 homolog a (hhr23a). [swissprot;acc:p54725] Divided 220.987 225.468 1.02028

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/