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 red Filtered green network_comparison
Results: HTML CSV LaTeX Showing element 51 to 100 of 16578 in total
Value Type  : Measured
Filtered  : 1
Rank
description
Network Comparison Type
Interaction Map
red
green
network_comparison
13 jumonji domain containing 1; zinc finger protein; testis-specific protein a. [refseq;acc:nm_018433] Divided Low confidence 1927.68 2959.19 1.5351
myosin vb (myosin 5b) (fragment). [swissprot;acc:q9ulv0] Subtracted High confidence 21591.5 27904.5 6313
14 homeobox protein hox-c5 (hox-3d) (cp11). [swissprot;acc:q00444] Low confidence 15464.1 17572.7 2108.6
myosin vc (myosin 5c). [swissprot;acc:q9nqx4] High confidence 21591.5 27904.5 6313
ras gtpase-activating protein ngap (ras protein activator like 1). [swissprot;acc:q9ujf2] Divided 398.5 1281.5 3.21581
trypsin iii precursor (ec 3.4.21.4) (brain trypsinogen) (mesotrypsinogen) (trypsin iv). [swissprot;acc:p35030] Low confidence 1972.65 2998.1 1.51983
15 homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] Subtracted 15464.1 17572.7 2108.6
myosin va (myosin 5a) (dilute myosin heavy chain, non-muscle) (myosin heavy chain 12) (myoxin). [swissprot;acc:q9y4i1] High confidence 21591.5 27904.5 6313
trypsin i precursor (ec 3.4.21.4) (cationic trypsinogen). [swissprot;acc:p07477] Divided Low confidence 1983.91 3007.85 1.51612
xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [refseq;acc:nm_007266] High confidence 2671 871 3.06659
16 28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5] Low confidence 21185 28492 1.34491
cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936] Subtracted High confidence 24260.3 18172.1 6088.2
homeobox protein hox-d4 (hox-4b) (hox-5.1) (hho.c13). [swissprot;acc:p09016] Low confidence 15464.1 17572.7 2108.6
protein x 0004. [refseq;acc:nm_016301] Divided High confidence 2671 871 3.06659
17 dgcr14 protein (digeorge syndrome critical region 14) (es2 protein). [swissprot;acc:q96df8] 460 1365 2.96739
homeobox protein hox-b5 (hox-2a) (hho.c10) (hu-1). [swissprot;acc:p09067] Subtracted Low confidence 15464.1 17572.7 2108.6
microtubule-associated proteins 1a/1b light chain 3b (map1a/map1b lc3 b) (map1a/1b light chain 3 b). [swissprot;acc:q9gzq8] High confidence 24255.7 18168.9 6086.8
mitochondrial solute carrier protein. [refseq;acc:nm_145305] Divided Low confidence 21185 28492 1.34491
18 cyclic-amp-dependent transcription factor atf-3 (activating transcription factor 3). [swissprot;acc:p18847] 5492.04 7251 1.32027
homeobox protein hox-a5 (hox-1c). [swissprot;acc:p20719] Subtracted 15464.1 17572.7 2108.6
microtubule-associated proteins 1a/1b light chain 3a (map1a/map1b lc3 a) (map1a/1b light chain 3 a). [swissprot;acc:q9h492] High confidence 24255.7 18168.9 6086.8
protein phosphatase 1, regulatory (inhibitor) subunit 14a; 17-kda pkc-potentiated inhibitory protein of pp1. [refseq;acc:nm_033256] Divided 677.5 1865.5 2.75351
19 25-hydroxyvitamin d-1 alpha hydroxylase, mitochondrial precursor (ec 1.14.-.-) (25-ohd-1 alpha-hydroxylase) (25-hydroxyvitamin d3 1- alpha-hydroxylase) (vd3 1a hydroxylase) (p450c1 alpha) (p450vd1- alpha). [swissprot;acc:o15528] Low confidence 3032.56 3915.4 1.29112
cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326] Subtracted High confidence 24250 18164.9 6085.1
homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056] Low confidence 15464.1 17572.7 2108.6
microfibril-associated glycoprotein 4 precursor. [swissprot;acc:p55083] Divided High confidence 677.5 1865.5 2.75351
20 gaba(a) receptor-associated protein; gaba(a)-receptor-associated protein. [refseq;acc:nm_007278] Subtracted 23421.5 17580.4 5841.1
protein phosphatase 1, regulatory subunit 14d; pkc-dependent pp1 inhibitory protein. [refseq;acc:nm_017726] Divided 677.5 1865.5 2.75351
retinal short-chain dehydrogenase/reductase 3. [refseq;acc:nm_016246] Subtracted Low confidence 15464.1 17572.7 2108.6
retinoblastoma-associated factor 600. [refseq;acc:nm_020765] Divided 7256.71 9368.87 1.29106
21 cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936] Subtracted 13689.1 11788.6 1900.5
cytochrome p450 27, mitochondrial precursor (ec 1.14.-.-) (cytochrome p-450c27/25) (sterol 26-hydroxylase) (sterol 27-hydroxylase) (vitamin d(3) 25-hydroxylase) (5-beta-cholestane-3-alpha,7-alpha,12-alpha-triol 27-hydroxylase). [swissprot;acc:q02318] Divided 3035.43 3917.88 1.29072
ficolin 2 precursor (collagen/fibrinogen domain-containing protein 2) (ficolin-b) (ficolin b) (serum lectin p35) (ebp-37) (hucolin) (l- ficolin). [swissprot;acc:q15485] High confidence 677.5 1865.5 2.75351
melanoma antigen, family d, 4 isoform 1; mage1 protein; mage-e1 protein; maged4 protein. [refseq;acc:nm_030801] Subtracted 23693.7 18263 5430.7
22 cytochrome p450 24a1, mitochondrial precursor (ec 1.14.-.-) (p450- cc24) (vitamin d(3) 24-hydroxylase) (1,25-dihydroxyvitamin d(3) 24- hydroxylase) (24-ohase). [swissprot;acc:q07973] Divided Low confidence 3126.88 3997.02 1.27828
hepatocellular carcinoma-associated protein hca3. [refseq;acc:nm_138703] Subtracted High confidence 23693.7 18263 5430.7
lysosome-associated membrane glycoprotein 1 precursor (lamp-1) (cd107a antigen). [swissprot;acc:p11279] Low confidence 2399.5 543.5 1856
protein phosphatase 1, regulatory (inhibitor) subunit 14c; serologically defined breast cancer antigen ny-br-81; pkc-potentiated pp1 inhibitory protein. [refseq;acc:nm_030949] Divided High confidence 677.5 1865.5 2.75351
23 carboxypeptidase d precursor (ec 3.4.17.-) (gp180). [swissprot;acc:o75976] Low confidence 40899 32028.5 1.27696
cell division protein kinase 4 (ec 2.7.1.37) (cyclin-dependent kinase 4) (psk-j3). [swissprot;acc:p11802] Subtracted 2399.5 543.5 1856
gbp protein isoform a. [refseq;acc:nm_017870] Divided High confidence 699.76 1894.39 2.7072
melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [swissprot;acc:p43357] Subtracted 23693.7 18263 5430.7
24 atlastin; guanylate-binding protein 3. [refseq;acc:nm_015915] Divided Low confidence 5720.25 4577.5 1.24965
cell division protein kinase 6 (ec 2.7.1.37) (serine/threonine protein kinase plstire). [swissprot;acc:q00534] Subtracted 2399.5 543.5 1856
melanoma-associated antigen 11 (mage-11 antigen). [swissprot;acc:p43364] High confidence 23693.7 18263 5430.7
protein kinase, interferon-inducible double stranded rna dependent activator; protein activator of the interferon-induced protein kinase. [refseq;acc:nm_003690] Divided 950.561 2108.52 2.21818
25 guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-7 subunit. [swissprot;acc:o60262] 1833.01 892.67 2.0534
histidine triad nucleotide-binding protein 1 (adenosine 5'- monophosphoramidase) (protein kinase c inhibitor 1) (protein kinase c- interacting protein 1) (pkci-1). [swissprot;acc:p49773] Low confidence 5847.46 4691.96 1.24627
lysosome-associated membrane glycoprotein 2 precursor (lamp-2) (cd107b antigen). [swissprot;acc:p13473] Subtracted 2399.5 543.5 1856
melanoma-associated antigen 2 (mage-2 antigen). [swissprot;acc:p43356] High confidence 23693.7 18263 5430.7

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/