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 962 to 1011 of 8289 in total
Value Type  : Measured
Network Comparison Type  : Divided
Filtered  : 1
Rank
description
Interaction Map
red
green
network_comparison
481 mitogen-activated protein kinase-activated protein kinase 3; mapkap kinase 3. [refseq;acc:nm_004635] High confidence 9649.61 11053.5 1.14549
482 acyl-coa dehydrogenase, very-long-chain specific, mitochondrial precursor (ec 1.3.99.-) (vlcad). [swissprot;acc:p49748] Low confidence 8350.58 8763.72 1.04947
mitogen-activated protein kinase 14 (ec 2.7.1.37) (mitogen-activated protein kinase p38alpha) (map kinase p38alpha) (cytokine suppressive anti-inflammatory drug binding protein) (csaid binding protein) (csbp) (max-interacting protein 2) (map kinase mxi2) (sapk2a). [swissprot;acc:q16539] High confidence 9649.61 11053.5 1.14549
483 cln3 protein (battenin) (batten disease protein). [swissprot;acc:q13286] Low confidence 7449.72 7818.1 1.04945
neuronal acetylcholine receptor protein, alpha-4 chain precursor. [swissprot;acc:p43681] High confidence 9649.61 11053.5 1.14549
484 likely ortholog of rat cytochrome p450 4x1. [refseq;acc:nm_178033] Low confidence 8193.5 8598.23 1.0494
neuronal acetylcholine receptor protein, alpha-3 chain precursor. [swissprot;acc:p32297] High confidence 9649.61 11053.5 1.14549
485 cytochrome p450 4b1 (ec 1.14.14.1) (cypivb1) (p450-hp). [swissprot;acc:p13584] Low confidence 8193.52 8598.28 1.0494
sphingosine kinase 2 (ec 2.7.1.-) (sk 2) (spk 2). [swissprot;acc:q9nra0] High confidence 9649.61 11053.5 1.14549
486 huntingtin interacting protein c. [refseq;acc:nm_012272] Low confidence 7802.39 8187.64 1.04938
stem cell growth factor; lymphocyte secreted c-type lectin; lymphocyte secreted c-type lectin. [refseq;acc:nm_002975] High confidence 10908.6 12491.8 1.14513
487 crooked neck-like protein 1 (crooked neck homolog) (hcrn) (cgi-201) (mstp021). [swissprot;acc:q9bzj0] Low confidence 7723.28 8104.43 1.04935
pyrroline 5-carboxylate reductase isoform. [refseq;acc:nm_013328] High confidence 5277.4 6042.88 1.14505
488 c-type lectin superfamily member 1 precursor (cartilage-derived c-type lectin). [swissprot;acc:o75596] 10872.4 12447 1.14483
pl6 protein (placental protein 6). [swissprot;acc:q12893] Low confidence 7939.82 8330.32 1.04918
489 pyrroline-5-carboxylate reductase (ec 1.5.1.2) (p5cr) (p5c reductase). [swissprot;acc:p32322] High confidence 5281.11 6044.61 1.14457
rgs19-interacting protein 1 (gaip c-terminus interacting protein gipc) (rgs-gaip interacting protein) (tax interaction protein 2) (tip-2). [swissprot;acc:o14908] Low confidence 7928.82 8318.74 1.04918
490 protein phosphatase 1, regulatory (inhibitor) subunit 13b; apoptosis-stimulating protein of p53, 1. [refseq;acc:nm_015316] High confidence 15274.9 13346.9 1.14445
ring finger protein 7; sensitive to apoptosis gene. [refseq;acc:nm_014245] Low confidence 7952.82 8343.96 1.04918
491 lysosomal-associated transmembrane protein 4 beta; putative integral membrane transporter. [refseq;acc:nm_018407] 7939.41 8329.89
neuron navigator 2 isoform l; retinoic acid inducible in neuroblastoma; pore membrane and/or filament interacting like protein 2; helicase helad1. [refseq;acc:nm_145117] High confidence 5980.15 6843.48 1.14437
492 lysosomal-associated transmembrane protein 4a (golgi 4-transmembrane spanning transporter mtp). [swissprot;acc:q15012] Low confidence 7939.82 8330.32 1.04918
neuron navigator 1; neuron navigator-1; pore membrane and/or filament interacting like protein 3. [refseq;acc:nm_020443] High confidence 5979.94 6842.76 1.14429
493 alanine aminotransferase (ec 2.6.1.2) (glutamic--pyruvic transaminase) (gpt) (glutamic--alanine transaminase). [swissprot;acc:p24298] Low confidence 8730.02 9159.19 1.04916
neuron navigator 3; pore membrane and/or filament interacting like protein 1; steerin 3. [refseq;acc:nm_014903] High confidence 5979.95 6842.78 1.14429
494 e2a-pbx1-associated protein; putative 47 kda protein. [refseq;acc:nm_020140] 5979.93 6842.72 1.14428
glioma-amplified sequence-41; numa binding protein 1. [refseq;acc:nm_006530] Low confidence 7615.76 7990.13 1.04916
495 dead/h (asp-glu-ala-asp/his) box polypeptide 11; dead/h box-11 (chl1-related helicase gene-1); yeast chl1 homolog. [refseq;acc:nm_030655] 9017.27 9460.22 1.04912
tetranectin precursor (tn) (plasminogen-kringle 4 binding protein). [swissprot;acc:p05452] High confidence 10804.7 12363.6 1.14428
496 helicase (fragment). [sptrembl;acc:q92771] Low confidence 9016.56 9459.33 1.04911
nostrin. [refseq;acc:nm_052946] High confidence 4682.87 4093.05 1.1441
497 dj18d14.4 (cytochrome p450, subfamily iva, polypeptide 11). [sptrembl;acc:q9ntl5] Low confidence 8180.34 8581.7 1.04906
eap30 subunit of ell complex. [refseq;acc:nm_007241] High confidence 4682.87 4093.05 1.1441
498 cytochrome p450 4a11 precursor (ec 1.14.15.3) (cypiva11) (fatty acid omega-hydroxylase) (p-450 hk omega) (lauric acid omega-hydroxylase) (cyp4aii) (p450-hl-omega). [swissprot;acc:q02928] Low confidence 8179.26 8580.38 1.04904
liv-1 protein, estrogen regulated. [refseq;acc:nm_012319] High confidence 4682.87 4093.05 1.1441
499 glutamate decarboxylase, 65 kda isoform (ec 4.1.1.15) (gad-65) (65 kda glutamic acid decarboxylase). [swissprot;acc:q05329]
trans-prenyltransferase; polyprenyl pyrophosphate synthetase. [refseq;acc:nm_014317] Low confidence 7267.76 7623.38 1.04893
500 gamma-soluble nsf attachment protein (snap-gamma) (n-ethylmaleimide- sensitive factor attachment protein, gamma). [swissprot;acc:q99747] High confidence 4682.87 4093.05 1.1441
mus81 endonuclease. [refseq;acc:nm_025128] Low confidence 8847.94 9279.83 1.04881
501 dpy-30-like protein. [swissprot;acc:q9c005] 8037.92 8430.24
glutamate decarboxylase, 67 kda isoform (ec 4.1.1.15) (gad-67) (67 kda glutamic acid decarboxylase). [swissprot;acc:q99259] High confidence 4682.87 4093.05 1.1441
502 ribonucleoside-diphosphate reductase m1 chain (ec 1.17.4.1) (ribonucleotide reductase large chain). [swissprot;acc:p23921] 6913.6 7907.05 1.1437
similar to hepatocellular carcinoma-associated antigen hca557b. [refseq;acc:nm_145280] Low confidence 8847.94 9279.83 1.04881
503 hepatocellularcarcinoma-associated antigen hca557a. [refseq;acc:nm_015433]
tumor suppressor p53-binding protein 2 (p53-binding protein 2) (53bp2) (bcl2-binding protein) (bbp). [swissprot;acc:q13625] High confidence 15182.5 13277.9 1.14344
504 enoyl-coa hydratase, mitochondrial precursor (ec 4.2.1.17) (short chain enoyl-coa hydratase) (sceh) (enoyl-coa hydratase 1). [swissprot;acc:p30084] 10067.9 11511 1.14334
protein cgi-100 precursor. [swissprot;acc:q9y3a6] Low confidence 9136.68 9582.26 1.04877
505 signal transduction protein cbl-b (sh3-binding protein cbl-b). [swissprot;acc:q13191] High confidence 6856.71 7838.3 1.14316
solute carrier family 13, member 3 (sodium-dependent high-affinity dicarboxylate transporter 2) (na(+)/dicarboxylate cotransporter 3) (nadc-3) (hnadc3). [swissprot;acc:q8wwt9] Low confidence 8890.93 9324.41 1.04876
506 eukaryotic translation initiation factor 6 (eif-6) (b4 integrin interactor) (cab) (p27(bbp)) (b(2)gcn homolog). [swissprot;acc:p56537] High confidence 3893.85 4450.98 1.14308

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/