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 Network Comparison Type Value Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 875 to 924 of 66312 in total
Filtered  : 1
Rank
Hugo
description
Network Comparison Type
Value Type
Interaction Map
red
green
network_comparison
55 PAPOLG poly(a) polymerase gamma (ec 2.7.7.19) (pap gamma) (polynucleotide adenylyltransferase gamma) (srp rna 3' adenylating enzyme). [swissprot;acc:q9bwt3] Subtracted Measured High confidence 23303.1 19279.5 4023.6
PPP1R14A protein phosphatase 1, regulatory (inhibitor) subunit 14a; 17-kda pkc-potentiated inhibitory protein of pp1. [refseq;acc:nm_033256] Rooted Low confidence 55.7075 63.2842 7.5767
PRKRAP1 protein kinase, interferon-inducible double stranded rna dependent activator; protein activator of the interferon-induced protein kinase. [refseq;acc:nm_003690] Divided Ranked High confidence 320.927 254.434 1.26134
PYGB glycogen phosphorylase, brain form (ec 2.4.1.1). [swissprot;acc:p11216] Subtracted 185.678 245.247 59.569
SEPT10 septin 10 isoform 1. [refseq;acc:nm_144710] Divided Measured Low confidence 13081.2 14872.6 1.13694
SEPT8 septin-like protein kiaa0202 (fragment). [swissprot;acc:q92599] Subtracted Squared 75490.8 95493.3 20002.5
56 no value guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-7 subunit. [swissprot;acc:o60262] Divided Ranked High confidence 266.856 336.233 1.25998
homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056] Squared Low confidence 122475 159767 1.30449
homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] Measured 15464.1 17572.7 1.13635
jun dimerization protein. [refseq;acc:nm_130469] Subtracted 6462.09 7593.77 1131.68
melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [swissprot;acc:p43357] Divided Squared High confidence 219048 129762 1.68808
CTH cystathionine gamma-lyase (ec 4.4.1.1) (gamma-cystathionase). [swissprot;acc:p32929] Rooted 41.6851 28.9509 1.43986
GSTO2 ba127l20.1 (novel glutathione-s-transferase). [sptrembl;acc:q9h4y5] Low confidence 62.7951 70.575 1.12389
HOXA5 homeobox protein hox-a5 (hox-1c). [swissprot;acc:p20719] Subtracted Squared High confidence 173408 242989 69581
MAGEB6B melanoma antigen, family b, 6. [refseq;acc:nm_173523] Rooted 137.446 120.823 16.623
MFAP4 microfibril-associated glycoprotein 4 precursor. [swissprot;acc:p55083] Low confidence 55.7075 63.2842 7.5767
PBK t-lak cell-originated protein kinase; spermatogenesis-related protein kinase; pdz-binding kinase; pbk; mapkk-like protein kinase; serine/threonine protein kinase. [refseq;acc:nm_018492] Divided Measured High confidence 1631.67 2664.55 1.63302
PYGL glycogen phosphorylase, liver form (ec 2.4.1.1). [swissprot;acc:p06737] Subtracted Ranked 185.678 245.247 59.569
RRAGA ras-related gtp binding a; ras-related gtp-binding protein. [refseq;acc:nm_006570] Measured 20911 24908.5 3997.5
SEPT10 septin 10 isoform 1. [refseq;acc:nm_144710] Squared Low confidence 74803.9 94281 19477.1
SMYD2 set and mynd domain containing 2; hskm-b protein; zinc finger, mynd domain containing 14. [refseq;acc:nm_020197] Ranked 230.944 209.149 21.795
T brachyury protein (t protein). [swissprot;acc:o15178] Divided 224.922 202.592 1.11022
57 no value homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056] Subtracted Squared High confidence 173408 242989 69581
melanoma-associated antigen 4 (mage-4 antigen) (mage-x2) (mage-41). [swissprot;acc:p43358] Rooted 137.446 120.823 16.623
FOS proto-oncogene protein c-fos (cellular oncogene fos) (g0/g1 switch regulatory protein 7). [swissprot;acc:p01100] Divided Ranked Low confidence 202.802 182.73 1.10985
FOSL2 fos-related antigen 2. [swissprot;acc:p15408] Subtracted Measured 6480.59 7600.25 1119.66
GNG12 guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-12 subunit. [swissprot;acc:q9ubi6] Divided Ranked High confidence 266.856 336.233 1.25998
GSTO1 glutathione transferase omega 1 (ec 2.5.1.18) (gsto 1-1). [swissprot;acc:p78417] Rooted Low confidence 63.0631 70.6746 1.1207
HOXB4 homeobox protein hox-b4 (hox-2f) (hox-2.6). [swissprot;acc:p17483] Measured 15464.1 17572.7 1.13635
HSD17B14 retinal short-chain dehydrogenase/reductase 3. [refseq;acc:nm_016246] Squared 122475 159767 1.30449
KCND3 potassium voltage-gated channel, shal-related subfamily, member 3 isoform 1; sha1-related potassium channel kv4.3; voltage-gated k+ channel; potassium ionic channel kv4.3; voltage-gated potassium channel kv4.3. [refseq;acc:nm_004980] Rooted High confidence 41.6879 28.9554 1.43973
KHDRBS3 kh domain containing, rna binding, signal transduction associated 3; sam68-like phosphotyrosine protein, t-star. [refseq;acc:nm_006558] Measured 1631.67 2664.55 1.63302
MAGEA11 melanoma-associated antigen 11 (mage-11 antigen). [swissprot;acc:p43364] Squared 219048 129762 1.68808
MYO15A myosin xv (unconventional myosin-15). [swissprot;acc:q9ukn7] Subtracted Ranked 185.678 245.247 59.569
PPP1R14D protein phosphatase 1, regulatory subunit 14d; pkc-dependent pp1 inhibitory protein. [refseq;acc:nm_017726] Rooted Low confidence 55.7075 63.2842 7.5767
RRAGC ras-related gtp binding c; rag c protein. [refseq;acc:nm_022157] Measured High confidence 20911 24908.5 3997.5
SEPT6 septin 6. [swissprot;acc:q14141] Squared Low confidence 74378.4 93531.9 19153.5
SMYD1 set and mynd domain containing protein 1. [sptrembl;acc:q8nb12] Ranked 230.944 209.149 21.795
58 no value jun dimerization protein. [refseq;acc:nm_130469] Divided 202.802 182.73 1.10985
ALDH4A1 delta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial precursor (ec 1.5.1.12) (p5c dehydrogenase). [swissprot;acc:p30038] Subtracted Squared 80538.1 64191.7 16346.4
FCN2 ficolin 2 precursor (collagen/fibrinogen domain-containing protein 2) (ficolin-b) (ficolin b) (serum lectin p35) (ebp-37) (hucolin) (l- ficolin). [swissprot;acc:q15485] Rooted 55.7075 63.2842 7.5767
FOSB protein fosb (g0/g1 switch regulatory protein 3). [swissprot;acc:p53539] Measured 6481.62 7600.61 1118.99
GNG4 guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-4 subunit. [swissprot;acc:p50150] Divided Ranked High confidence 266.863 336.191 1.25979
HOXC5 homeobox protein hox-c5 (hox-3d) (cp11). [swissprot;acc:q00444] Measured Low confidence 15464.1 17572.7 1.13635
HSD17B14 retinal short-chain dehydrogenase/reductase 3. [refseq;acc:nm_016246] Subtracted Squared High confidence 173408 242989 69581
KCND1 potassium voltage-gated channel, shal-related subfamily, member 1; shal-type potassium channel; voltage-gated potassium channel kv4.1. [refseq;acc:nm_004979] Divided Rooted 41.6969 28.9696 1.43933
KHDRBS1 kh domain containing, rna binding, signal transduction associated 1; gap-associated tyrosine phosphoprotein p62 (sam68). [refseq;acc:nm_006559] Measured 1631.67 2664.55 1.63302
MAGEA2B melanoma-associated antigen 2 (mage-2 antigen). [swissprot;acc:p43356] Squared 219048 129762 1.68808
MAGEA9 melanoma-associated antigen 9 (mage-9 antigen). [swissprot;acc:p43362] Subtracted Rooted 137.446 120.823 16.623
NDUFA12 nadh-ubiquinone oxidoreductase subunit b17.2 (ec 1.6.5.3) (ec 1.6.99.3) (complex i-b17.2) (ci-b17.2) (cib17.2) (13 kda differentiation-associated protein). [swissprot;acc:q9ui09] Divided Low confidence 59.0909 66.1317 1.11915

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/