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 red green Filtered network_comparison
Results: HTML CSV LaTeX Showing element 51 to 100 of 16578 in total
Value Type  : Measured
Filtered  : 1
Rank
Network Comparison Type
description
Interaction Map
red
green
network_comparison
13 Subtracted homeobox protein hox-b4 (hox-2f) (hox-2.6). [swissprot;acc:p17483] Low confidence 15464.1 17572.7 2108.6
myosin vb (myosin 5b) (fragment). [swissprot;acc:q9ulv0] High confidence 21591.5 27904.5 6313
14 Divided ras gtpase-activating protein ngap (ras protein activator like 1). [swissprot;acc:q9ujf2] 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
Subtracted homeobox protein hox-c5 (hox-3d) (cp11). [swissprot;acc:q00444] 15464.1 17572.7 2108.6
myosin vc (myosin 5c). [swissprot;acc:q9nqx4] High confidence 21591.5 27904.5 6313
15 Divided trypsin i precursor (ec 3.4.21.4) (cationic trypsinogen). [swissprot;acc:p07477] 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
Subtracted homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] Low confidence 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
16 Divided 28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5] Low confidence 21185 28492 1.34491
protein x 0004. [refseq;acc:nm_016301] High confidence 2671 871 3.06659
Subtracted cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936] 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
17 Divided dgcr14 protein (digeorge syndrome critical region 14) (es2 protein). [swissprot;acc:q96df8] High confidence 460 1365 2.96739
mitochondrial solute carrier protein. [refseq;acc:nm_145305] Low confidence 21185 28492 1.34491
Subtracted homeobox protein hox-b5 (hox-2a) (hho.c10) (hu-1). [swissprot;acc:p09067] 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
18 Divided cyclic-amp-dependent transcription factor atf-3 (activating transcription factor 3). [swissprot;acc:p18847] Low confidence 5492.04 7251 1.32027
protein phosphatase 1, regulatory (inhibitor) subunit 14a; 17-kda pkc-potentiated inhibitory protein of pp1. [refseq;acc:nm_033256] High confidence 677.5 1865.5 2.75351
Subtracted homeobox protein hox-a5 (hox-1c). [swissprot;acc:p20719] Low confidence 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
19 Divided 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
microfibril-associated glycoprotein 4 precursor. [swissprot;acc:p55083] High confidence 677.5 1865.5 2.75351
Subtracted cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326] 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
20 Divided protein phosphatase 1, regulatory subunit 14d; pkc-dependent pp1 inhibitory protein. [refseq;acc:nm_017726] High confidence 677.5 1865.5 2.75351
retinoblastoma-associated factor 600. [refseq;acc:nm_020765] Low confidence 7256.71 9368.87 1.29106
Subtracted gaba(a) receptor-associated protein; gaba(a)-receptor-associated protein. [refseq;acc:nm_007278] High confidence 23421.5 17580.4 5841.1
retinal short-chain dehydrogenase/reductase 3. [refseq;acc:nm_016246] Low confidence 15464.1 17572.7 2108.6
21 Divided 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] 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
Subtracted cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936] Low confidence 13689.1 11788.6 1900.5
melanoma antigen, family d, 4 isoform 1; mage1 protein; mage-e1 protein; maged4 protein. [refseq;acc:nm_030801] High confidence 23693.7 18263 5430.7
22 Divided 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] Low confidence 3126.88 3997.02 1.27828
protein phosphatase 1, regulatory (inhibitor) subunit 14c; serologically defined breast cancer antigen ny-br-81; pkc-potentiated pp1 inhibitory protein. [refseq;acc:nm_030949] High confidence 677.5 1865.5 2.75351
Subtracted hepatocellular carcinoma-associated protein hca3. [refseq;acc:nm_138703] 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
23 Divided carboxypeptidase d precursor (ec 3.4.17.-) (gp180). [swissprot;acc:o75976] 40899 32028.5 1.27696
gbp protein isoform a. [refseq;acc:nm_017870] High confidence 699.76 1894.39 2.7072
Subtracted cell division protein kinase 4 (ec 2.7.1.37) (cyclin-dependent kinase 4) (psk-j3). [swissprot;acc:p11802] Low confidence 2399.5 543.5 1856
melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [swissprot;acc:p43357] High confidence 23693.7 18263 5430.7
24 Divided atlastin; guanylate-binding protein 3. [refseq;acc:nm_015915] Low confidence 5720.25 4577.5 1.24965
protein kinase, interferon-inducible double stranded rna dependent activator; protein activator of the interferon-induced protein kinase. [refseq;acc:nm_003690] High confidence 950.561 2108.52 2.21818
Subtracted cell division protein kinase 6 (ec 2.7.1.37) (serine/threonine protein kinase plstire). [swissprot;acc:q00534] Low confidence 2399.5 543.5 1856
melanoma-associated antigen 11 (mage-11 antigen). [swissprot;acc:p43364] High confidence 23693.7 18263 5430.7
25 Divided 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
Subtracted lysosome-associated membrane glycoprotein 2 precursor (lamp-2) (cd107b antigen). [swissprot;acc:p13473] 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/