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 Value Type description Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 3658 to 3707 of 6456 in total
Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1
Rank
Hugo
description
Network Comparison Type
red
green
network_comparison
1829 NSUN5B williams beuren syndrome chromosome region 20c isoform 1. [refseq;acc:nm_032158] Subtracted 223.862 226.271 2.409
1830 PFKM 6-phosphofructokinase, muscle type (ec 2.7.1.11) (phosphofructokinase 1) (phosphohexokinase) (phosphofructo-1-kinase isozyme a) (pfk-a) (phosphofructokinase-m). [swissprot;acc:p08237] Divided 240.32 243.069 1.01144
POLDIP2 dna polymerase delta p38 subunit. [refseq;acc:nm_015584] Subtracted 222.819 225.228 2.409
1831 no value f-actin capping protein alpha-2 subunit (capz alpha-2). [swissprot;acc:p47755] Divided 214.746 212.328 1.01139
EIF2B4 translation initiation factor eif-2b delta subunit (eif-2b gdp-gtp exchange factor). [swissprot;acc:q9ui10] Subtracted 221.725 224.133 2.408
1832 EIF2S3 eukaryotic translation initiation factor 2 subunit 3 (eukaryotic translation initiation factor 2 gamma subunit) (eif-2-gamma). [swissprot;acc:p41091] 221.639 224.046 2.407
SLC4A1AP solute carrier family 4 (anion exchanger), member 1, adaptor protein; kidney anion exchanger adaptor protein; kanadaptin; lung cancer oncogene 3. [refseq;acc:nm_018158] Divided 180.409 182.459 1.01136
1833 CKS2 cyclin-dependent kinases regulatory subunit 2 (cks-2). [swissprot;acc:p33552]
TOP2B dna topoisomerase ii, beta isozyme (ec 5.99.1.3). [swissprot;acc:q02880] Subtracted 203.759 201.357 2.402
1834 CTNNAL1 catenin (cadherin-associated protein), alpha-like 1; alpha-catulin. [refseq;acc:nm_003798] Divided 180.409 182.459 1.01136
ERCC2 tfiih basal transcription factor complex helicase subunit (ec 3.6.1.-) (dna-repair protein complementing xp-d cells) (xeroderma pigmentosum group d complementing protein) (cxpd) (dna excision repair protein ercc-2). [swissprot;acc:p18074] Subtracted 188.452 190.845 2.393
1835 no value brain protein 16. [refseq;acc:nm_016458] 216.811 219.195 2.384
GORASP2 golgi reassembly stacking protein 2; golgi reassembly stacking protein 2, 55 kda. [refseq;acc:nm_015530] Divided 194.573 192.396 1.01132
1836 BAAT bile acid coenzyme a: amino acid n-acyltransferase; glycine n-choloyltransferase. [refseq;acc:nm_001701] Subtracted 218.441 216.064 2.377
RPIA ribose 5-phosphate isomerase (ec 5.3.1.6) (phosphoriboisomerase). [swissprot;acc:p49247] Divided 208.821 211.17 1.01125
1837 ABI2 abl-interactor 2; abl-interacting protein 1 (sh3-containing protein); abl binding protein 3; arg protein tyrosine kinase-binding protein; abl-interactor protein 2b; similar to spectrin sh3 domain binding protein 1. [refseq;acc:nm_005759] Subtracted 217.077 214.702 2.375
KHK ketohexokinase (ec 2.7.1.3) (hepatic fructokinase). [swissprot;acc:p50053] Divided 218.984 221.446 1.01124
1838 no value purine nucleoside phosphorylase (ec 2.4.2.1) (inosine phosphorylase) (pnp). [swissprot;acc:p00491]
CDA cytidine deaminase (ec 3.5.4.5) (cytidine aminohydrolase). [swissprot;acc:p32320] Subtracted 220.852 223.225 2.373
1839 ACOT1 peroxisomal acyl-coenzyme a thioester hydrolase 2a (ec 3.1.2.2) (peroxisomal long-chain acyl-coa thioesterase 2) (zap128). [swissprot;acc:p49753] 218.445 216.074 2.371
EIF2S2 eukaryotic translation initiation factor 2 subunit 2 (eukaryotic translation initiation factor 2 beta subunit) (eif-2-beta). [swissprot;acc:p20042] Divided 221.525 224.001 1.01118
1840 ACOT4 peroxisomal acyl-coa thioesterase 2b; likely ortholog of mouse peroxisomal acyl-coa thioesterase 2b. [refseq;acc:nm_152331] Subtracted 218.448 216.08 2.368
APEX1 dna-(apurinic or apyrimidinic site) lyase (ec 4.2.99.18) (ap endonuclease 1) (apex nuclease) (apen) (ref-1 protein). [swissprot;acc:p27695] Divided 211.882 209.544 1.01116
1841 ABI1 spectrin sh3 domain binding protein 1; eps8 binding protein; interactor protein ablbp4; abl-interactor protein 1 long; nap1 binding protein. [refseq;acc:nm_005470] Subtracted 217.066 214.698 2.368
PARL presenilins associated rhomboid-like protein. [refseq;acc:nm_018622] Divided 212.455 210.113 1.01115
1842 BBOX1 gamma-butyrobetaine,2-oxoglutarate dioxygenase (ec 1.14.11.1) (gamma-butyrobetaine hydroxylase) (gamma-bbh). [swissprot;acc:o75936]
TTL tubulin-tyrosine ligase. [refseq;acc:nm_153712] Subtracted 217.924 215.564 2.36
1843 ATP11A potential phospholipid-transporting atpase ih (ec 3.6.3.1) (atpase class i type 11a) (atpase is). [swissprot;acc:p98196] Divided 212.455 210.113 1.01115
LANCL2 lanc lantibiotic synthetase component c-like 2; testis-specific adriamycin sensitivity protein; lanc (bacterial lantibiotic synthetase component c)-like 2; g protein-coupled receptor 69b. [refseq;acc:nm_018697] Subtracted 220.107 217.75 2.357
1844 LANCL1 lanthionine synthetase c-like protein 1; g protein-coupled receptor 69a; lanc (bacterial lantibiotic synthetase component c)-like 1; lanc (bacterial lantibiotic synthetase component). [refseq;acc:nm_006055]
PAX6 paired box protein pax-6 (oculorhombin) (aniridia, type ii protein). [swissprot;acc:p26367] Divided 214.773 212.417 1.01109
1845 ABI2 abl-interactor 2; abl-interacting protein 1 (sh3-containing protein); abl binding protein 3; arg protein tyrosine kinase-binding protein; abl-interactor protein 2b; similar to spectrin sh3 domain binding protein 1. [refseq;acc:nm_005759] 217.077 214.702 1.01106
PAX6 paired box protein pax-6 (oculorhombin) (aniridia, type ii protein). [swissprot;acc:p26367] Subtracted 214.773 212.417 2.356
1846 ABI1 spectrin sh3 domain binding protein 1; eps8 binding protein; interactor protein ablbp4; abl-interactor protein 1 long; nap1 binding protein. [refseq;acc:nm_005470] Divided 217.066 214.698 1.01103
RPIA ribose 5-phosphate isomerase (ec 5.3.1.6) (phosphoriboisomerase). [swissprot;acc:p49247] Subtracted 208.821 211.17 2.349
1847 no value brain protein 16. [refseq;acc:nm_016458] Divided 216.811 219.195 1.011
GRSF1 g-rich sequence factor-1 (grsf-1). [swissprot;acc:q12849] Subtracted 217.891 215.542 2.349
1848 BAAT bile acid coenzyme a: amino acid n-acyltransferase; glycine n-choloyltransferase. [refseq;acc:nm_001701] Divided 218.441 216.064 1.011
HNRPH3 heterogeneous nuclear ribonucleoprotein h3 (hnrnp h3) (hnrnp 2h9). [swissprot;acc:p31942] Subtracted 217.892 215.543 2.349
1849 ACOT1 peroxisomal acyl-coenzyme a thioester hydrolase 2a (ec 3.1.2.2) (peroxisomal long-chain acyl-coa thioesterase 2) (zap128). [swissprot;acc:p49753] Divided 218.445 216.074 1.01097
HNRPF heterogeneous nuclear ribonucleoprotein f (hnrnp f). [swissprot;acc:p52597] Subtracted 217.893 215.545 2.348
1850 CAP1 adenylyl cyclase-associated protein 1 (cap 1). [swissprot;acc:q01518] Divided 215.931 213.587 1.01097
HNRPH1 heterogeneous nuclear ribonucleoprotein h (hnrnp h). [swissprot;acc:p31943] Subtracted 217.895 215.547 2.348
1851 ACOT4 peroxisomal acyl-coa thioesterase 2b; likely ortholog of mouse peroxisomal acyl-coa thioesterase 2b. [refseq;acc:nm_152331] Divided 218.448 216.08 1.01096
HNRPH2 heterogeneous nuclear ribonucleoprotein h' (hnrnp h') (ftp-3). [swissprot;acc:p55795] Subtracted 217.895 215.547 2.348
1852 no value 3-hydroxyisobutyryl-coenzyme a hydrolase. [refseq;acc:nm_014362] Divided 196.008 198.154 1.01095
CAP1 adenylyl cyclase-associated protein 1 (cap 1). [swissprot;acc:q01518] Subtracted 215.931 213.587 2.344
1853 PARL presenilins associated rhomboid-like protein. [refseq;acc:nm_018622] 212.455 210.113 2.342
TTL tubulin-tyrosine ligase. [refseq;acc:nm_153712] Divided 217.924 215.564 1.01095
1854 BBOX1 gamma-butyrobetaine,2-oxoglutarate dioxygenase (ec 1.14.11.1) (gamma-butyrobetaine hydroxylase) (gamma-bbh). [swissprot;acc:o75936] Subtracted 212.455 210.113 2.342

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/