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 description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 4308 to 4357 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
Network Comparison Type
red
green
network_comparison
539 myosin heavy chain, skeletal muscle, adult 2 (myosin heavy chain iia) (myhc-iia). [swissprot;acc:q9ukx2] Ranked Subtracted 112 126 14
pef protein with a long n-terminal hydrophobic domain (peflin). [refseq;acc:nm_012392] Rooted 62.9281 67.99 5.0619
protein cgi-27 (c21orf19-like protein). [swissprot;acc:q9y316] Ranked Divided 236.964 252.86 1.06708
thymus-specific serine protease precursor (ec 3.4.-.-). [swissprot;acc:q9nqe7] Measured 10603.5 12069.4 1.13825
werner helicase interacting protein isoform 1; putative helicase ruvbl; werner helicase interacting protein. [refseq;acc:nm_020135] Squared 20613.1 24595.9 1.19322
540 argininosuccinate lyase (ec 4.3.2.1) (arginosuccinase) (asal). [swissprot;acc:p04424] 26048.6 31057.4 1.19229
gamma-aminobutyric-acid receptor gamma-3 subunit precursor (gaba(a) receptor). [swissprot;acc:q99928] Rooted 66.082 71.6526 1.0843
gk001 protein. [refseq;acc:nm_020198] Measured 10603.5 12069.4 1.13825
keratin associated protein 9-4; keratin associated protein 9.4. [refseq;acc:nm_033191] Squared Subtracted 31099.4 36082.4 4983
pantothenate kinase 3 (ec 2.7.1.33) (pantothenic acid kinase 3) (hpank3). [swissprot;acc:q9h999] Ranked 58 44 14
putative adenosylhomocysteinase 2 (ec 3.3.1.1) (s-adenosyl-l- homocysteine hydrolase) (adohcyase). [swissprot;acc:o43865] Measured 6228.39 7013.19 784.8
selenide,water dikinase 2 (ec 2.7.9.3) (selenophosphate synthetase 2) (selenium donor protein 2). [swissprot;acc:q99611] Ranked Divided 222.156 208.201 1.06703
swi/snf-related, matrix-associated, actin-dependent regulator of chromatin subfamily f member 1 (swi-snf complex protein p270) (b120). [swissprot;acc:o14497] Rooted Subtracted 64.5685 69.6269 5.0584
541 calsyntenin-2 precursor. [swissprot;acc:q9h4d0] Measured Divided 10600.3 12065.2 1.13819
coatomer beta subunit (beta-coat protein) (beta-cop). [swissprot;acc:p53618] Squared 53774.6 45105.5 1.1922
flavoprotein oxidoreductase mical2. [refseq;acc:nm_014632] Ranked 222.156 208.201 1.06703
forkhead box protein g1c (forkhead-related protein fkhl3) (hfk3) (fragment). [swissprot;acc:q14488] Rooted 66.082 71.6526 1.0843
limkain b1. [refseq;acc:nm_019081] Measured Subtracted 6228.39 7013.19 784.8
myosin heavy chain, fast skeletal muscle, embryonic (muscle embryonic myosin heavy chain) (smhce). [swissprot;acc:p11055] Ranked 112 126 14
programmed cell death protein 6 (probable calcium-binding protein alg- 2). [swissprot;acc:o75340] Rooted 64.5685 69.6269 5.0584
protein cgi-147. [swissprot;acc:q9y3e5] Squared 36787.9 31806.3 4981.6
542 brg1-binding protein eld/osa1; eld (eyelid)/osa protein. [refseq;acc:nm_020732] Rooted 64.5672 69.6254 5.0582
gamma-aminobutyric-acid receptor gamma-1 subunit precursor (gaba(a) receptor). [swissprot;acc:q8n1c3] Divided 66.082 71.6526 1.0843
inositol polyphosphate-4-phosphatase, type ii, 105kd; inositol polyphosphate 4-phosphatase ii; 4-phosphatase ii. [refseq;acc:nm_003866] Ranked 222.156 208.201 1.06703
myosin heavy chain, skeletal muscle, adult 1 (myosin heavy chain iix/d) (myhc-iix/d). [swissprot;acc:p12882] Subtracted 112 126 14
putative adenosylhomocysteinase 3 (ec 3.3.1.1) (s-adenosyl-l- homocysteine hydrolase) (adohcyase). [swissprot;acc:q96hn2] Measured 6228.39 7013.19 784.8
rac-alpha serine/threonine kinase (ec 2.7.1.-) (rac-pk-alpha) (protein kinase b) (pkb) (c-akt). [swissprot;acc:p31749] Divided 3889.27 4426.74 1.13819
ran binding protein 11. [refseq;acc:nm_016338] Squared Subtracted 26018.9 30994.1 4975.2
s-adenosylmethionine synthetase alpha and beta forms (ec 2.5.1.6) (methionine adenosyltransferase) (adomet synthetase) (mat-i/iii). [swissprot;acc:q00266] Divided 26084.2 31084.3 1.19169
543 calsyntenin-3 precursor. [swissprot;acc:q9bqt9] Measured 10599.9 12064.7 1.13819
cellular repressor of e1a-stimulated genes. [refseq;acc:nm_003851] Subtracted 6228.39 7013.19 784.8
gamma-aminobutyric-acid receptor alpha-2 subunit precursor (gaba(a) receptor). [swissprot;acc:p47869] Rooted Divided 66.082 71.6525 1.0843
glutamate carboxypeptidase-like protein 2 precursor. [swissprot;acc:q96kn2] Squared 26612.5 31709 1.19151
grancalcin. [swissprot;acc:p28676] Rooted Subtracted 64.5659 69.624 5.0581
membrane protein expressed in epithelial-like lung adenocarcinoma. [refseq;acc:nm_024792] Squared 26010 30981.7 4971.7
myosin heavy chain, cardiac muscle beta isoform (myhc-beta). [swissprot;acc:p12883] Ranked 112 126 14
selenide,water dikinase 1 (ec 2.7.9.3) (selenophosphate synthetase 1) (selenium donor protein 1). [swissprot;acc:p49903] Divided 222.156 208.201 1.06703
544 3-hydroxyisobutyryl-coenzyme a hydrolase. [refseq;acc:nm_014362] Squared Subtracted 27898 32866.2 4968.2
disks large-associated protein 3 (dap-3) (sap90/psd-95-associated protein 3) (sapap3) (psd-95/sap90 binding protein 3) (fragment). [swissprot;acc:o95886] Measured 6228.39 7013.19 784.8
dj756n5.1.1 (continues in em:al133324 as dj1161h23.3) (fragment). [sptrembl;acc:q9h430] Ranked 112 126 14
gamma-aminobutyric-acid receptor alpha-6 subunit precursor (gaba(a) receptor). [swissprot;acc:q16445] Rooted Divided 66.082 71.6525 1.0843
inositol polyphosphate-4-phosphatase, type 1 isoform b; inositol polyphosphate-4-phosphatase, type i, 107kd; 4-phosphatase i; inositol polyphosphate-4-phosphatase i. [refseq;acc:nm_001566] Ranked 222.156 208.201 1.06703
rac-gamma serine/threonine protein kinase (ec 2.7.1.-) (rac-pk-gamma) (protein kinase akt-3) (protein kinase b, gamma) (pkb gamma) (stk-2). [swissprot;acc:q9y243] Measured 3889.27 4426.74 1.13819
ran binding protein 11. [refseq;acc:nm_016338] Squared 26018.9 30994.1 1.19121
sorcin (22 kda protein) (cp-22) (v19). [swissprot;acc:p30626] Rooted Subtracted 64.566 69.6241 5.0581
545 calcium-dependent protease, small subunit (calpain regulatory subunit) (calcium-activated neutral proteinase) (canp). [swissprot;acc:p04632] 64.5657 69.6237 5.058
eukaryotic translation initiation factor 6 (eif-6) (b4 integrin interactor) (cab) (p27(bbp)) (b(2)gcn homolog). [swissprot;acc:p56537] Ranked Divided 248.866 233.287 1.06678
gamma-aminobutyric-acid receptor gamma-2 subunit precursor (gaba(a) receptor). [swissprot;acc:p18507] Rooted 66.082 71.6526 1.0843
kininogen precursor (alpha-2-thiol proteinase inhibitor) [contains: bradykinin]. [swissprot;acc:p01042] Measured Subtracted 6228.39 7013.19 784.8
membrane protein expressed in epithelial-like lung adenocarcinoma. [refseq;acc:nm_024792] Squared Divided 26010 30981.7 1.19115

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/