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 10714 to 10763 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
green
network_comparison
2679 beta-soluble nsf attachment protein (snap-beta) (n-ethylmaleimide- sensitive factor attachment protein, beta). [swissprot;acc:q9h115] Squared 24123.5 24679.6 1.02305
rho guanine nucleotide exchange factor 6 (pak-interacting exchange factor alpha) (alpha-pix) (cool-2). [swissprot;acc:q15052] Measured 5358.78 5384.44 1.00479
tumor protein d54 (hd54) (d52-like 2). [swissprot;acc:o43399] Rooted 66.0973 65.8527 1.00371
2680 reticulon protein 3 (neuroendocrine-specific protein-like 2) (nsp-like protein ii) (nsplii). [swissprot;acc:o95197] 65.5654 65.7881 1.0034
serine/threonine-protein kinase pak 3 (ec 2.7.1.-) (p21-activated kinase 3) (pak-3) (beta-pak) (oligophrenin-3). [swissprot;acc:o75914] Measured 5358.3 5383.94 1.00479
syntaxin 16 (syn16). [swissprot;acc:o14662] Squared 24123.5 24679.6 1.02305
transforming protein p21/h-ras-1 (c-h-ras). [swissprot;acc:p01112] Ranked 144.422 144.56 1.00096
2681 27 kda golgi snare protein (golgi snap receptor complex member 2) (membrin). [swissprot;acc:o14653] Squared 24123.5 24679.6 1.02305
ribosomal protein s27-like protein; 40s ribosomal protein s27 isoform. [refseq;acc:nm_015920] Rooted 56.6829 56.8734 1.00336
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] Measured 5358.31 5383.94 1.00478
ubiquitin-specific protease otubain 2. [refseq;acc:nm_023112] Ranked 203.592 203.787 1.00096
2682 40s ribosomal protein s27 (metallopan-stimulin 1) (mps-1). [swissprot;acc:p42677] Rooted 56.6826 56.8729 1.00336
conserved oligomeric golgi complex subunit 5 (13s golgi transport complex 90 kda subunit) (gtc-90) (golgi transport complex 1). [swissprot;acc:q9up83] Measured 5358.3 5383.93 1.00478
syntaxin 1a (neuron-specific antigen hpc-1). [swissprot;acc:q16623] Squared 24123.5 24679.6 1.02305
transforming protein n-ras. [swissprot;acc:p01111] Ranked 144.427 144.564 1.00095
2683 alpha-soluble nsf attachment protein (snap-alpha) (n-ethylmaleimide- sensitive factor attachment protein, alpha). [swissprot;acc:p54920] Squared 24123.5 24679.6 1.02305
nuclease sensitive element binding protein 1 (y box binding protein-1) (y-box transcription factor) (yb-1) (ccaat-binding transcription factor i subunit a) (cbf-a) (enhancer factor i subunit a) (efi-a) (dna-binding protein b) (dbpb). [swissprot;acc:p16991] Ranked 208.438 208.635 1.00095
reticulon protein 2 (neuroendocrine-specific protein-like 1) (nsp-like protein 1) (nspli). [swissprot;acc:o75298] Rooted 65.5639 65.7815 1.00332
serine/threonine-protein kinase pak 1 (ec 2.7.1.-) (p21-activated kinase 1) (pak-1) (p65-pak) (alpha-pak). [swissprot;acc:q13153] Measured 5358.3 5383.93 1.00478
2684 adipocyte plasma membrane-associated protein (bscv protein). [swissprot;acc:q9hdc9] Squared 24123.5 24679.6 1.02305
dna-binding protein a (cold shock domain protein a) (single-strand dna binding protein nf-gmb). [swissprot;acc:p16989] Ranked 208.438 208.635 1.00095
rho guanine nucleotide exchange factor 7 (pak-interacting exchange factor beta) (beta-pix) (cool-1) (p85). [swissprot;acc:q14155] Measured 5357.73 5383.33 1.00478
zinc finger protein 174 (aw-1). [swissprot;acc:q15697] Rooted 44.5817 44.4359 1.00328
2685 cytochrome c1, heme protein, mitochondrial precursor (cytochrome c-1). [swissprot;acc:p08574] Measured 3953.53 3972.32 1.00475
germ cell specific y-box binding protein; contrin. [refseq;acc:nm_015982] Ranked 208.438 208.635 1.00095
reticulon 1 (neuroendocrine-specific protein). [swissprot;acc:q16799] Rooted 65.5679 65.7824 1.00327
synaptosomal-associated protein 29 (snap-29) (vesicle-membrane fusion protein snap-29) (soluble 29 kda nsf attachment protein). [swissprot;acc:o95721] Squared 24123.5 24679.6 1.02305
2686 oligophrenin-1 like protein (gtpase regulator associated with focal adhesion kinase). [swissprot;acc:q9una1] Measured 3953.53 3972.32 1.00475
proteasome subunit beta type 7 precursor (ec 3.4.25.1) (proteasome subunit z) (macropain chain z) (multicatalytic endopeptidase complex chain z). [swissprot;acc:q99436] Ranked 219.829 219.629 1.00091
syntaxin 1b. [swissprot;acc:q15531] Squared 24123.5 24679.6 1.02305
zinc finger imprinted 2. [swissprot;acc:q9nzv7] Rooted 44.5831 44.4382 1.00326
2687 branched-chain amino acid aminotransferase, mitochondrial precursor (ec 2.6.1.42) (bcat(m)) (placental protein 18) (pp18). [swissprot;acc:o15382] Ranked 210.939 210.755 1.00087
eh-domain containing protein 1 (testilin) (hpast1). [swissprot;acc:q9h4m9] Rooted 65.5658 65.7794 1.00326
melanoma antigen p15 (melanoma-associated antigen recognized by t lymphocytes). [swissprot;acc:q13084] Squared 24123.5 24679.6 1.02305
senescence marker protein-30 (smp-30) (regucalcin) (rc). [swissprot;acc:q15493] Measured 3953.53 3972.32 1.00475
2688 dna-binding protein rfxank (regulatory factor x subunit b) (rfx-b) (ankyrin repeat family a protein 1). [swissprot;acc:o14593] Squared 24123.5 24679.6 1.02305
eh-domain containing protein 4 (eh domain-containing protein fksg7) (hepatocellular carcinoma-associated protein 10/11). [swissprot;acc:q9h223] Rooted 65.5659 65.7792 1.00325
oligophrenin 1. [swissprot;acc:o60890] Measured 3953.53 3972.32 1.00475
peroxisomal 3,2-trans-enoyl-coa isomerase (ec 5.3.3.8) (dodecenoyl-coa delta-isomerase) (d3,d2-enoyl-coa isomerase) (dbi-related protein 1) (drs-1) (hepatocellular carcinoma-associated antigen 88). [swissprot;acc:o75521] Ranked 194.557 194.392 1.00085
2689 atp-citrate synthase (ec 2.3.3.8) (atp-citrate (pro-s-)-lyase) (citrate cleavage enzyme). [swissprot;acc:p53396] 213.792 213.619 1.00081
eh-domain containing protein 2. [swissprot;acc:q9nzn4] Rooted 65.5659 65.7792 1.00325
neuropilin- and tolloid-like protein 2 precursor. [refseq;acc:nm_018092] Measured 4113.79 4095.53 1.00446
nucleoporin-like protein rip (hiv-1 rev-binding protein) (rev interacting protein) (rev/rex activation domain-binding protein). [swissprot;acc:p52594] Squared 22249 22757.3 1.02285
2690 aquaporin 4 (wch4) (mercurial-insensitive water channel) (miwc). [swissprot;acc:p55087] Ranked 188.191 188.046 1.00077
eh-domain containing protein 3. [swissprot;acc:q9nzn3] Rooted 65.5659 65.7793 1.00325
intersectin 1 (sh3 domain-containing protein 1a) (sh3p17). [swissprot;acc:q15811] Squared 22249 22757.3 1.02285
neuropilin- and tolloid-like protein 1 isoform 3 precursor. [refseq;acc:nm_138966] Measured 4113.79 4095.53 1.00446
2691 aquaporin-cd (aqp-cd) (water channel protein for renal collecting duct) (adh water channel) (aquaporin 2) (collecting duct water channel protein) (wch-cd). [swissprot;acc:p41181] Ranked 188.193 188.048 1.00077
heterogenous nuclear ribonucleoprotein u (hnrnp u) (scaffold attachment factor a) (saf-a). [swissprot;acc:q00839] Measured 4113.79 4095.53 1.00446
pram-1 protein; pml-rara target gene encoding an adaptor molecule-1. [refseq;acc:nm_032152] Squared 22249 22757.3 1.02285

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/