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 Network Comparison Type Gene Value Type description Interaction Map green red Filtered network_comparison
Results: HTML CSV LaTeX Showing element 2513 to 2562 of 16578 in total
Value Type  : Measured
Filtered  : 1
Rank
Network Comparison Type
description
Interaction Map
green
red
network_comparison
629 Divided cellular repressor of e1a-stimulated genes. [refseq;acc:nm_003851] High confidence 7013.19 6228.39 1.126
g10 protein homolog (edg-2). [swissprot;acc:p41223] Low confidence 8288.53 7932.4 1.0449
Subtracted breast cancer antiestrogen resistance 3. [refseq;acc:nm_003567] 8183.05 7826.34 356.71
neuronal acetylcholine receptor protein, alpha-7 chain precursor. [swissprot;acc:p36544] High confidence 4479.76 5201.41 721.65
630 Divided disks large-associated protein 3 (dap-3) (sap90/psd-95-associated protein 3) (sapap3) (psd-95/sap90 binding protein 3) (fragment). [swissprot;acc:o95886] 7013.19 6228.39 1.126
glutamyl trna synthetase. [sptrembl;acc:o14563] Low confidence 8723.11 8348.4 1.04488
Subtracted adenylate cyclase, type vi (ec 4.6.1.1) (atp pyrophosphate-lyase) (ca(2+)-inhibitable adenylyl cyclase). [swissprot;acc:o43306] High confidence 4479.76 5201.41 721.65
phosphatidylinositol-4-phosphate 5-kinase, type i, beta. [refseq;acc:nm_003558] Low confidence 9060.03 8703.47 356.56
631 Divided 17-beta-hydroxysteroid dehydrogenase type vii-like. [refseq;acc:nm_182829] 8689.28 8316.12 1.04487
kininogen precursor (alpha-2-thiol proteinase inhibitor) [contains: bradykinin]. [swissprot;acc:p01042] High confidence 7013.19 6228.39 1.126
Subtracted adenylate cyclase, type v (ec 4.6.1.1) (atp pyrophosphate-lyase) (adenylyl cyclase) (fragment). [swissprot;acc:o95622] 4479.76 5201.41 721.65
g10 protein homolog (edg-2). [swissprot;acc:p41223] Low confidence 8288.53 7932.4 356.13
632 Divided disks large-associated protein 2 (dap-2) (sap90/psd-95-associated protein 2) (sapap2) (psd-95/sap90 binding protein 2) (fragment). [swissprot;acc:q9p1a6] High confidence 7013.19 6228.39 1.126
estradiol 17 beta-dehydrogenase 7 (ec 1.1.1.62) (17-beta-hsd 7) (17- beta-hydroxysteroid dehydrogenase 7). [swissprot;acc:p56937] Low confidence 8688.21 8315.33 1.04484
Subtracted leucine-rich repeat-containing protein 15 precursor (hlib). [swissprot;acc:q8tf66] High confidence 4479.76 5201.41 721.65
mitogen-activated protein kinase kinase kinase 3 (ec 2.7.1.-) (mapk/erk kinase kinase 3) (mek kinase 3) (mekk 3). [swissprot;acc:q99759] Low confidence 8636.93 8281.14 355.79
633 Divided ferritin light chain (ferritin l subunit). [swissprot;acc:p02792] High confidence 7013.19 6228.39 1.126
tpa regulated locus; uncharacterized hypothalamus protein htmp. [refseq;acc:nm_018475] Low confidence 8704.52 8331.28 1.0448
Subtracted fem-1 homolog b; fem-1-like death receptor binding protein; fem-1 (c.elegans) homolog b. [refseq;acc:nm_015322] High confidence 4479.76 5201.41 721.65
trans-prenyltransferase; polyprenyl pyrophosphate synthetase. [refseq;acc:nm_014317] Low confidence 7623.38 7267.76 355.62
634 Divided ba526d8.2 (novel protein similar to kiaa1074). [sptrembl;acc:q9h560] 7587.85 7262.59 1.04479
disks large-associated protein 4 (dap-4) (sap90/psd-95-associated protein 4) (sapap4) (psd-95/sap90 binding protein 4). [swissprot;acc:q9y2h0] High confidence 7013.19 6228.39 1.126
Subtracted leucine-rich repeat protein lrrc3 precursor. [swissprot;acc:q9by71] 4479.76 5201.41 721.65
mitogen-activated protein kinase kinase kinase 2 (ec 2.7.1.-) (mapk/erk kinase kinase 2) (mek kinase 2) (mekk 2). [swissprot;acc:q9y2u5] Low confidence 8635.76 8280.29 355.47
635 Divided ankyrin repeat domain protein 7 (testis-specific protein tsa806). [swissprot;acc:q92527] 7587.39 7262.13 1.04479
ferritin heavy polypeptide-like 17. [swissprot;acc:q9bxu8] High confidence 7013.53 6228.97 1.12595
Subtracted contactin 2 precursor (axonin-1) (axonal glycoprotein tag-1) (transient axonal glycoprotein 1) (tax-1). [swissprot;acc:q02246] Low confidence 8509.76 8154.34 355.42
laminin gamma-1 chain precursor (laminin b2 chain). [swissprot;acc:p11047] High confidence 4479.76 5201.41 721.65
636 Divided breast cancer antigen ny-br-1. [refseq;acc:nm_052997] Low confidence 7587.97 7262.73 1.04478
proteasome subunit alpha type 5 (ec 3.4.25.1) (proteasome zeta chain) (macropain zeta chain) (multicatalytic endopeptidase complex zeta chain). [swissprot;acc:p28066] High confidence 6432.92 5713.41 1.12593
Subtracted contactin 5 isoform long; neural adhesion molecule. [refseq;acc:nm_014361] Low confidence 8509.76 8154.34 355.42
thymic stromal co-transporter. [refseq;acc:nm_033051] High confidence 4479.76 5201.41 721.65
637 Divided putative nucleoside diphosphate kinase (ec 2.7.4.6) (ndk) (ndp kinase). [swissprot;acc:o60361] 8731.76 7756.51 1.12573
ubiquitin-conjugating enzyme e2 m (ec 6.3.2.19) (ubiquitin-protein ligase m) (ubiquitin carrier protein m) (nedd8-conjugating enzyme ubc12). [swissprot;acc:o76069] Low confidence 8384.21 8025.21 1.04473
Subtracted contactin 6; neural adhesion molecule. [refseq;acc:nm_014461] 8509.76 8154.34 355.42
l-myc-1 proto-oncogene protein. [swissprot;acc:p12524] High confidence 5610.52 4889.21 721.31
638 Divided nucleoside diphosphate kinase a (ec 2.7.4.6) (ndk a) (ndp kinase a) (tumor metastatic process-associated protein) (metastasis inhibition factor nm23) (nm23-h1). [swissprot;acc:p15531] 8730.74 7755.69 1.12572
tryptophan 2,3-dioxygenase (ec 1.13.11.11) (tryptophan pyrrolase) (tryptophanase) (tryptophan oxygenase) (tryptamin 2,3-dioxygenase) (trpo). [swissprot;acc:p48775] Low confidence 8065.07 7720 1.0447
Subtracted n-myc proto-oncogene protein. [swissprot;acc:p04198] High confidence 5610.69 4889.71 720.98
putative homeodomain transcription factor 1. [swissprot;acc:q9ums5] Low confidence 8509.76 8154.34 355.42
639 Divided nucleolysin tiar (tia-1 related protein). [swissprot;acc:q01085] 8029.54 7686.11 1.04468
nucleoside diphosphate kinase b (ec 2.7.4.6) (ndk b) (ndp kinase b) (nm23-h2) (c-myc purine-binding transcription factor puf). [swissprot;acc:p22392] High confidence 8728.13 7753.59 1.12569
Subtracted ga binding protein alpha chain (gabp-alpha subunit) (transcription factor e4tf1-60) (nuclear respiratory factor-2 subunit alpha). [swissprot;acc:q06546] 5610.95 4890.51 720.44
mg81 protein (fragment). [sptrembl;acc:q14830] Low confidence 8509.76 8154.34 355.42
640 Divided glutathione s-transferase theta 2 (ec 2.5.1.18) (gst class-theta). [swissprot;acc:p30712] High confidence 5414.64 4811.02 1.12547
membrane-associated nucleic acid binding protein. [refseq;acc:nm_018835] Low confidence 6881.19 6586.97 1.04467
Subtracted contactin precursor (glycoprotein gp135). [swissprot;acc:q12860] 8509.76 8154.34 355.42
ga binding protein beta-2 chain (gabp-beta-2 subunit) (transcription factor e4tf1-47) (gapbp-2) (nuclear respiratory factor-2 subunit gamma). [swissprot;acc:q06545] High confidence 5610.95 4890.51 720.44
641 Divided cox15 homolog isoform 2 precursor; cytochrome c oxidase subunit 15; cytochrome c oxidase assembly protein. [refseq;acc:nm_004376] Low confidence 8476.88 8114.52 1.04466
peroxisomal n1-acetyl-spermine/spermidine oxidase. [refseq;acc:nm_152911] High confidence 5414.21 4810.85 1.12542

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/