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 Interaction Map Network Comparison Type Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 2832 to 2881 of 6456 in total
Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1
Rank
Hugo
description
Network Comparison Type
red
green
network_comparison
1416 WDFY2 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 ASAH1 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
CPA5 carboxypeptidase a5. [refseq;acc:nm_080385] Divided 203.979 208.229 1.02084
1418 CPB1 carboxypeptidase b precursor (ec 3.4.17.2) (pancreas-specific protein) (pasp). [swissprot;acc:p15086]
CRX cone-rod homeobox protein. [swissprot;acc:o43186] Subtracted 244.331 240.061 4.27
1419 OTX1 homeobox protein otx1. [swissprot;acc:p32242] 244.367 240.098 4.269
SLC3A1 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 ACY1 aminoacylase-1 (ec 3.5.1.14) (n-acyl-l-amino-acid amidohydrolase) (acy-1). [swissprot;acc:q03154]
OTX2 homeobox protein otx2. [swissprot;acc:p32243] Subtracted 244.478 240.212 4.266
1421 ASAH1 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
CPA5 carboxypeptidase a5. [refseq;acc:nm_080385] Subtracted 203.979 208.229 4.25
1422 CPA1 carboxypeptidase a1 precursor (ec 3.4.17.1). [swissprot;acc:p15085] Divided 1.02084
CPB1 carboxypeptidase b precursor (ec 3.4.17.2) (pancreas-specific protein) (pasp). [swissprot;acc:p15086] Subtracted 4.25
1423 no value cysteine-rich protein 1 (cysteine-rich intestinal protein) (crip) (cysteine-rich heart protein) (hcrhp). [swissprot;acc:p50238] Divided 221.152 216.659 1.02074
SLC3A1 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 ACY1 aminoacylase-1 (ec 3.5.1.14) (n-acyl-l-amino-acid amidohydrolase) (acy-1). [swissprot;acc:q03154]
ATP1A1 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 CPA1 carboxypeptidase a1 precursor (ec 3.4.17.1). [swissprot;acc:p15085] Subtracted 203.979 208.229 4.25
CTSL2 cathepsin l2 precursor (ec 3.4.22.43) (cathepsin v) (cathepsin u). [swissprot;acc:o60911] Divided 214.717 219.157 1.02068
1426 CTSL1 cathepsin l precursor (ec 3.4.22.15) (major excreted protein) (mep). [swissprot;acc:p07711]
PTRH2 protein cgi-147. [swissprot;acc:q9y3e5] Subtracted 221.961 226.186 4.225
1427 ATP1A3 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
CSNK1A1L casein kinase i alpha s-like. [refseq;acc:nm_145203] Subtracted 229.459 225.237 4.222
1428 ATP1A2 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
CSNK1A1 casein kinase i, alpha isoform (ec 2.7.1.-) (cki-alpha) (ck1). [swissprot;acc:p48729] Subtracted 229.459 225.237 4.222
1429 QARS glutaminyl-trna synthetase (ec 6.1.1.18) (glutamine--trna ligase) (glnrs). [swissprot;acc:p47897] 221.412 217.199 4.213
WDR26 wd repeat domain 26. [refseq;acc:nm_025160] Divided 213.351 217.74 1.02057
1430 DUT deoxyuridine 5'-triphosphate nucleotidohydrolase, mitochondrial precursor (ec 3.6.1.23) (dutpase) (dutp pyrophosphatase). [swissprot;acc:p33316] 187.114 190.925 1.02037
SRM spermidine synthase (ec 2.5.1.16) (putrescine aminopropyltransferase) (spdsy). [swissprot;acc:p19623] Subtracted 221.412 217.199 4.213
1431 GARS glycyl-trna synthetase (ec 6.1.1.14) (glycine--trna ligase) (glyrs). [swissprot;acc:p41250]
RAD23A uv excision repair protein rad23 homolog a (hhr23a). [swissprot;acc:p54725] Divided 220.987 225.468 1.02028
1432 EARS2 glutamyl trna synthetase. [sptrembl;acc:o14563] Subtracted 221.412 217.199 4.213
PSMD4 26s proteasome non-atpase regulatory subunit 4 (26s proteasome regulatory subunit s5a) (rpn10) (multiubiquitin chain binding protein) (antisecretory factor-1) (af) (asf). [swissprot;acc:p55036] Divided 220.987 225.468 1.02028
1433 LSAMP limbic system-associated membrane protein precursor (lsamp). [swissprot;acc:q13449] Subtracted 224.354 220.15 4.204
OCRL inositol polyphosphate 5-phosphatase ocrl-1 (ec 3.1.3.36) (lowe's oculocerebrorenal syndrome protein). [swissprot;acc:q01968] Divided 220.987 225.468 1.02028
1434 no value poly (adp-ribose) glycohydrolase. [refseq;acc:nm_003631] Subtracted 217.351 213.18 4.171
RAD23B uv excision repair protein rad23 homolog b (hhr23b) (xp-c repair complementing complex 58 kda protein) (p58). [swissprot;acc:p54727] Divided 220.987 225.468 1.02028
1435 no value myosin vi. [swissprot;acc:q9um54]
MTO1 mto1 protein homolog (cgi-02). [swissprot;acc:q9y2z2] Subtracted 217.351 213.18 4.171
1436 EVI5L similar to ecotropic viral integration site 5; neuroblastoma stage 4s gene. [refseq;acc:nm_145245] Divided 218.829 214.493 1.02022
RANBP5 importin beta-3 subunit (karyopherin beta-3 subunit) (ran-binding protein 5). [swissprot;acc:o00410] Subtracted 218.582 214.427 4.155
1437 EVI5 ecotropic viral integration site 5; neuroblastoma stage 4s gene. [refseq;acc:nm_005665] Divided 218.829 214.493 1.02022
PYCR2 pyrroline 5-carboxylate reductase isoform. [refseq;acc:nm_013328] Subtracted 172.365 168.219 4.146
1438 PGGT1B geranylgeranyl transferase type i beta subunit (ec 2.5.1.-) (type i protein geranyl-geranyltransferase beta subunit) (ggtase-i-beta). [swissprot;acc:p53609] Divided 225.039 229.573 1.02015
UBE2E1 ubiquitin-conjugating enzyme e2 e1 (ec 6.3.2.19) (ubiquitin-protein ligase e1) (ubiquitin carrier protein e1) (ubch6). [swissprot;acc:p51965] Subtracted 166.846 170.989 4.143
1439 FADS3 fatty acid desaturase 3; linoleoyl-coa desaturase (delta-6-desaturase)-like 3; delta-6 fatty acid desaturase. [refseq;acc:nm_021727] Divided 225.039 229.573 1.02015
UBE2E4P ubiquitin-conjugating enzyme e2e 3; ubiquitin carrier protein; ubiquitin-protein ligase. [refseq;acc:nm_006357] Subtracted 166.846 170.989 4.143
1440 OPCML opioid binding protein/cell adhesion molecule precursor (obcam) (opioid-binding cell adhesion molecule) (opcml). [swissprot;acc:q14982] 224.159 220.017 4.142
SMAD4 mothers against decapentaplegic homolog 4 (smad 4) (mothers against dpp homolog 4) (deletion target in pancreatic carcinoma 4) (hsmad4). [swissprot;acc:q13485] Divided 225.039 229.573 1.02015
1441 FADS2 fatty acid desaturase 2; linoleoyl-coa desaturase (delta-6-desaturase)-like 2; delta-6 fatty acid desaturase. [refseq;acc:nm_004265]

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/