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 975 to 1024 of 8289 in total
Value Type  : Ranked
Network Comparison Type  : Divided
Filtered  : 1
Rank
description
Interaction Map
red
green
network_comparison
488 skeletal muscle tropomodulin (sk-tmod) (tropomodulin 4). [swissprot;acc:q9nzq9] Low confidence 209.136 202.478 1.03288
squamous cell carcinoma antigen recognized by t cells 1; u4/u6.u5 tri-snrnp-associated 110 kda protein; ige autoantigen; sart1(259) protein; sart1(800) protein. [refseq;acc:nm_005146] High confidence 225.026 209.798 1.07258
489 protein phosphatase 2c beta isoform (ec 3.1.3.16) (pp2c-beta). [swissprot;acc:o75688] 231.276 215.627 1.07257
ubiquitous tropomodulin (u-tmod) (tropomodulin 3). [swissprot;acc:q9nyl9] Low confidence 209.136 202.478 1.03288
490 rho guanine nucleotide exchange factor 7 (pak-interacting exchange factor beta) (beta-pix) (cool-1) (p85). [swissprot;acc:q14155] High confidence 220.183 236.015 1.0719
tropomodulin 1 (erythrocyte tropomodulin) (e-tmod). [swissprot;acc:p28289] Low confidence 209.136 202.478 1.03288
491 nucleolar gtp-binding protein 1 (chronic renal failure gene protein) (gtp-binding protein ngb). [swissprot;acc:q9bze4] High confidence 251.83 234.951 1.07184
sorting nexin 9 (sh3 and px domain-containing protein 1) (sdp1 protein). [swissprot;acc:q9y5x1] Low confidence 209.136 202.478 1.03288
492 neuronal tropomodulin (n-tmod) (tropomodulin 2). [swissprot;acc:q9nzr1]
serine/threonine-protein kinase pak 2 (ec 2.7.1.-) (p21-activated kinase 2) (pak-2) (pak65) (gamma-pak) (s6/h4 kinase). [swissprot;acc:q13177] High confidence 220.171 235.979 1.0718
493 activated p21cdc42hs kinase. [refseq;acc:nm_005781] Low confidence 209.136 202.478 1.03288
conserved oligomeric golgi complex subunit 5 (13s golgi transport complex 90 kda subunit) (gtc-90) (golgi transport complex 1). [swissprot;acc:q9up83] High confidence 220.172 235.98 1.0718
494 elongation factor 1-beta (ef-1-beta). [swissprot;acc:p24534] Low confidence 206.154 199.596 1.03286
serine/threonine-protein kinase pak 1 (ec 2.7.1.-) (p21-activated kinase 1) (pak-1) (p65-pak) (alpha-pak). [swissprot;acc:q13153] High confidence 220.172 235.98 1.0718
495 lim domains containing 1. [refseq;acc:nm_014240] Low confidence 203.117 196.671 1.03278
serine/threonine-protein kinase pak 3 (ec 2.7.1.-) (p21-activated kinase 3) (pak-3) (beta-pak) (oligophrenin-3). [swissprot;acc:o75914] High confidence 220.171 235.979 1.0718
496 probable mitochondrial import receptor subunit tom7 homolog (translocase of outer membrane 7 kda subunit homolog) (protein ad- 014). [swissprot;acc:q9p0u1] Low confidence 203.117 196.671 1.03278
suppressor of swi4 1 homolog (ssf-1) (peter pan homolog). [swissprot;acc:q9nq55] High confidence 250.938 234.134 1.07177
497 probable rrna processing protein ebp2 (ebna1 binding protein 2) (nucleolar protein p40). [swissprot;acc:q99848] 251.344 234.514
splicing factor 4 isoform b; rna-binding protein. [refseq;acc:nm_021164] Low confidence 203.117 196.671 1.03278
498 kinesin-associated protein 3 (smg gds-associated protein). [swissprot;acc:q92845]
rho guanine nucleotide exchange factor 6 (pak-interacting exchange factor alpha) (alpha-pix) (cool-2). [swissprot;acc:q15052] High confidence 220.161 235.95 1.07172
499 polymerase (dna directed) iota; rad30 (s. cerevisiae) homolog b; polymerase (dna-directed), iota. [refseq;acc:nm_007195] Low confidence 203.167 196.732 1.03271
triosephosphate isomerase (ec 5.3.1.1) (tim). [swissprot;acc:p00938] High confidence 231.496 248.048 1.0715
500 inhibitor of growth family, member 1-like; inhibitor of growth 1-like. [refseq;acc:nm_001564] 224.662 240.673 1.07127
rna 3'-terminal phosphate cyclase-like protein (hspc338). [swissprot;acc:q9y2p8] Low confidence 203.85 197.403 1.03266
501 calcyphosine. [swissprot;acc:q13938] 204.363 197.899
cytochrome c1, heme protein, mitochondrial precursor (cytochrome c-1). [swissprot;acc:p08574] High confidence 238.704 255.68 1.07112
502 oligophrenin-1 like protein (gtpase regulator associated with focal adhesion kinase). [swissprot;acc:q9una1]
squamous cell carcinoma antigen recognized by t cells 1; u4/u6.u5 tri-snrnp-associated 110 kda protein; ige autoantigen; sart1(259) protein; sart1(800) protein. [refseq;acc:nm_005146] Low confidence 200.271 193.957 1.03255
503 senescence marker protein-30 (smp-30) (regucalcin) (rc). [swissprot;acc:q15493] High confidence 238.704 255.68 1.07112
ubiquitin carboxyl-terminal hydrolase 22 (ec 3.1.2.15) (ubiquitin thiolesterase 22) (ubiquitin-specific processing protease 22) (deubiquitinating enzyme 22) (fragment). [swissprot;acc:q9upt9] Low confidence 207.407 200.869 1.03255
504 oligophrenin 1. [swissprot;acc:o60890] High confidence 238.704 255.68 1.07112
zinc finger protein 183. [swissprot;acc:o15541] Low confidence 205.192 198.726 1.03254
505 ad24 protein. [refseq;acc:nm_022451] High confidence 251.334 234.672 1.071
proliferating cell nuclear antigen (pcna) (cyclin). [swissprot;acc:p12004] Low confidence 207.84 201.297 1.0325
506 inhibitor of growth family, member 1; inhibitor of growth 1. [refseq;acc:nm_005537] High confidence 224.535 240.476 1.071
putative fork head domain transcription factor afx1 (forkhead box protein o4). [swissprot;acc:p98177] Low confidence 205.157 198.715 1.03242
507 hemoglobin gamma-a and gamma-g chains. [swissprot;acc:p02096]
wd-repeat protein 12 (ytm1 homolog). [swissprot;acc:q9gzl7] High confidence 251.299 234.729 1.07059
508 amyloid beta a4 protein precursor (app) (abpp) (alzheimer's disease amyloid protein) (cerebral vascular amyloid peptide) (cvap) (protease nexin-ii) (pn-ii) (appi) (prea4) [contains: soluble app-alpha (s-app- alpha); soluble app-beta (s-app-beta); c99; beta-amyloid protein 42 (beta-app42); beta-amyloid protein 40 (beta-app40); c83; p3(42); p3(40); gamma-ctf(59) (gamma-secretase c-terminal fragment 59) (amyloid intracellular domain 59) (aid(59)); gamma-ctf(57) (gamma- secretase c-terminal fragment 57) (amyloid intracellular domain 57) (aid(57)); gamma-ctf(50) (gamma-secretase c-terminal fragment 50) (amyloid intracellular domain 50) (aid(50)); c31]. [swissprot;acc:p05067] Low confidence 205.157 198.715 1.03242
mast cell carboxypeptidase a precursor (ec 3.4.17.1) (mc-cpa) (carboxypeptidase a3). [swissprot;acc:p15088] High confidence 177.698 190.24 1.07058
509 carboxypeptidase b precursor. [refseq;acc:nm_020361] 190.239 1.07057
tweety homolog 2. [refseq;acc:nm_032646] Low confidence 205.157 198.715 1.03242
510 hemoglobin zeta chain (hbaz). [swissprot;acc:p02008]
plasma carboxypeptidase b2 isoform a preproprotein; carboxypeptidase u; thrombin-activatable fibrinolysis inhibitor; carboxypeptidase b-like protein; thrombin-activable fibrinolysis inhibitor. [refseq;acc:nm_001872] High confidence 177.699 190.24 1.07057
511 alpha 2 globin. [refseq;acc:nm_000517] Low confidence 205.157 198.715 1.03242
proliferating-cell nucleolar antigen p120 (proliferation-associated nucleolar protein p120). [swissprot;acc:p46087] High confidence 250.053 233.725 1.06986
512 amyloid-like protein 1 precursor (aplp) (aplp-1) [contains: c30]. [swissprot;acc:p51693] Low confidence 205.157 198.715 1.03242
block of proliferation 1. [swissprot;acc:q14137] High confidence 250.794 234.433 1.06979

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/