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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Gene Rank description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 6358 to 6407 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
Network Comparison Type
red
green
network_comparison
795 serpin b11. [swissprot;acc:q96p15] Ranked Divided 224.244 234.511 1.04578
target of myb1-like 2; target of myb1 (chicken) homolog-like 2. [refseq;acc:nm_144678] Measured Subtracted 5641.53 6256.17 614.64
tbc1 domain family member 5. [swissprot;acc:q92609] Rooted 65.0565 69.1533 4.0968
796 beta-soluble nsf attachment protein (snap-beta) (n-ethylmaleimide- sensitive factor attachment protein, beta). [swissprot;acc:q9h115] Ranked 212.386 221.785 9.399
branched-chain amino acid aminotransferase, mitochondrial precursor (ec 2.6.1.42) (bcat(m)) (placental protein 18) (pp18). [swissprot;acc:o15382] Squared 23966.4 27952.2 3985.8
integral membrane protein 2b (transmembrane protein bri) [contains: abri/adan amyloid peptide]. [swissprot;acc:q9y287] Measured 6362.64 6976.1 613.46
nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7] Divided 6834.54 7590.49 1.11061
placental thrombin inhibitor (cytoplasmic antiproteinase) (cap) (protease inhibitor 6) (pi-6). [swissprot;acc:p35237] Ranked 224.244 234.511 1.04578
set domain and mariner transposase fusion gene. [refseq;acc:nm_006515] Rooted 54.765 51.4319 1.06481
tubby related protein 1 (tubby-like protein 1). [swissprot;acc:o00294] Subtracted 65.0565 69.1533 4.0968
xpmc2 prevents mitotic catastrophe 2 homolog; xenopus prevents mitotic catastrophe 2 homolog. [refseq;acc:nm_020385] Squared Divided 25842.1 30093.4 1.16451
797 cytoplasmic antiproteinase 2 (cap2) (cap-2) (protease inhibitor 8) (serpin b8). [swissprot;acc:p50452] Ranked 224.244 234.511 1.04578
importin beta-1 subunit (karyopherin beta-1 subunit) (nuclear factor p97) (importin 90). [swissprot;acc:q14974] Measured 6834.54 7590.49 1.11061
integral membrane protein 2c (transmembrane protein bri3) (npd018). [swissprot;acc:q9nqx7] Subtracted 6362.64 6976.1 613.46
limbic system-associated membrane protein precursor (lsamp). [swissprot;acc:q13449] Squared Divided 22535.2 26238.4 1.16433
structure-specific recognition protein 1 (ssrp1) (recombination signal sequence recognition protein) (t160) (chromatin-specific transcription elongation factor 80 kda subunit) (fact 80 kda subunit). [swissprot;acc:q08945] Rooted 54.1622 57.6725 1.06481
syntaxin 16 (syn16). [swissprot;acc:o14662] Ranked Subtracted 212.386 221.785 9.399
transcription factor p65 (nuclear factor nf-kappa-b p65 subunit). [swissprot;acc:q04206] Squared 46338.5 42353.5 3985
vacuolar protein sorting 29 (vesicle protein sorting 29) (hvps29) (mds007) (pep11) (dc7/dc15). [swissprot;acc:q9ubq0] Rooted 65.0565 69.1533 4.0968
798 27 kda golgi snare protein (golgi snap receptor complex member 2) (membrin). [swissprot;acc:o14653] Ranked 212.386 221.785 9.399
cd209 antigen-like; putative type ii membrane protein. [refseq;acc:nm_014257] Rooted Divided 54.765 51.4319 1.06481
integral membrane protein 2a (e25 protein). [swissprot;acc:o43736] Measured Subtracted 6362.64 6976.1 613.46
leukocyte elastase inhibitor (lei) (monocyte/neutrophil elastase inhibitor) (m/nei) (ei). [swissprot;acc:p30740] Ranked Divided 224.244 234.511 1.04578
numb-like protein (numb-r). [swissprot;acc:q9y6r0] Rooted Subtracted 65.0565 69.1533 4.0968
opioid binding protein/cell adhesion molecule precursor (obcam) (opioid-binding cell adhesion molecule) (opcml). [swissprot;acc:q14982] Squared Divided 22587.2 26296.1 1.1642
transcription factor relb (i-rel). [swissprot;acc:q01201] Subtracted 46338.5 42353.5 3985
transducin beta-like 1x protein (transducin-beta-like 1, x-linked). [swissprot;acc:o60907] Measured Divided 6834.54 7590.49 1.11061
799 dihydropyrimidine dehydrogenase [nadp+] precursor (ec 1.3.1.2) (dpd) (dhpdhase) (dihydrouracil dehydrogenase) (dihydrothymine dehydrogenase). [swissprot;acc:q12882] Subtracted 5222.71 5834.57 611.86
low affinity immunoglobulin epsilon fc receptor (lymphocyte ige receptor) (fc-epsilon-rii) (cd23) (blast-2) (immunoglobulin e-binding factor). [swissprot;acc:p06734] Rooted Divided 54.765 51.4319 1.06481
neurotrimin precursor (hnt). [swissprot;acc:q9p121] Squared 22623.7 26336.8 1.16412
nf-kappab inhibitor alpha (major histocompatibility complex enhancer- binding protein mad3) (i-kappa-b-alpha) (ikappabalpha) (ikb-alpha). [swissprot;acc:p25963] Subtracted 46338.5 42353.5 3985
sequestosome 1; ubiquitin-binding protein p62; phosphotyrosine independent ligand for the lck sh2 domain p62. [refseq;acc:nm_003900] Ranked Divided 221.965 212.404 1.04501
syntaxin 1a (neuron-specific antigen hpc-1). [swissprot;acc:q16623] Subtracted 212.386 221.785 9.399
transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87] Measured Divided 6834.54 7590.49 1.11061
tubby related protein 3 (tubby-like protein 3). [swissprot;acc:o75386] Rooted Subtracted 65.0565 69.1533 4.0968
800 alpha-soluble nsf attachment protein (snap-alpha) (n-ethylmaleimide- sensitive factor attachment protein, alpha). [swissprot;acc:p54920] Ranked 212.386 221.785 9.399
ccaat-box-binding transcription factor (ccaat-binding factor) (cbf). [swissprot;acc:q03701] Measured 3583.56 4194.95 611.39
chromatin-specific transcription elongation factor large subunit. [refseq;acc:nm_007192] Rooted Divided 54.1622 57.6725 1.06481
coproporphyrinogen iii oxidase, mitochondrial precursor (ec 1.3.3.3) (coproporphyrinogenase) (coprogen oxidase) (cox). [swissprot;acc:p36551] Squared Subtracted 46338.5 42353.5 3985
nonspecific lipid-transfer protein, mitochondrial precursor (nsl-tp) (sterol carrier protein 2) (scp-2) (sterol carrier protein x) (scp-x) (scpx). [swissprot;acc:p22307] Ranked Divided 221.965 212.404 1.04501
orphan nuclear receptor nr6a1 (germ cell nuclear factor) (gcnf) (retinoid receptor-related testis specific receptor) (rtr). [swissprot;acc:q15406] Measured 6075.55 6746.92 1.1105
phosphomannomutase 2 (ec 5.4.2.8) (pmm 2). [swissprot;acc:o15305] Squared 22210.6 25839.9 1.1634
vacuolar protein sorting 35 (vesicle protein sorting 35) (hvps35) (maternal-embryonic 3). [swissprot;acc:q96qk1] Rooted Subtracted 65.0565 69.1533 4.0968
801 adipocyte plasma membrane-associated protein (bscv protein). [swissprot;acc:q9hdc9] Ranked 212.386 221.785 9.399
beta-catenin (pro2286). [swissprot;acc:p35222] Divided 224.445 214.894 1.04445
cd209 antigen; dendritic cell-specific icam3-grabbing nonintegrin. [refseq;acc:nm_021155] Rooted 54.765 51.4319 1.06481
importin alpha-3 subunit (karyopherin alpha-3 subunit) (srp1-gamma). [swissprot;acc:o00505] Measured 6456.35 7169.75 1.1105
neurogenic differentiation factor 2 (neurod2). [swissprot;acc:q15784] Subtracted 779.167 1390.33 611.163
phosphomannomutase 1 (ec 5.4.2.8) (pmm 1) (pmmh-22). [swissprot;acc:q92871] Squared Divided 22208.7 25833.6 1.16322
protein kinase c, zeta type (ec 2.7.1.37) (npkc-zeta). [swissprot;acc:q05513] Rooted Subtracted 65.0565 69.1533 4.0968

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/