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.


Navigation/Query Panel:
Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].
Rank Gene Value Type Interaction Map description Network Comparison Type Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 1 to 50 of 8289 in total
Value Type  : Measured
Network Comparison Type  : Divided
Filtered  : 1
Rank
Interaction Map
description
red
green
network_comparison
1 High confidence rad50-interacting protein 1. [refseq;acc:nm_021930] 450.5 2394.5 5.31521
Low confidence lysosome-associated membrane glycoprotein 1 precursor (lamp-1) (cd107a antigen). [swissprot;acc:p11279] 2399.5 543.5 4.4149
2 High confidence rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6] 450.5 2394.5 5.31521
Low confidence cell division protein kinase 4 (ec 2.7.1.37) (cyclin-dependent kinase 4) (psk-j3). [swissprot;acc:p11802] 2399.5 543.5 4.4149
3 High confidence homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774] 2597.5 698.5 3.71868
Low confidence cell division protein kinase 6 (ec 2.7.1.37) (serine/threonine protein kinase plstire). [swissprot;acc:q00534] 2399.5 543.5 4.4149
4 High confidence hbs1-like. [refseq;acc:nm_006620] 2597.5 698.5 3.71868
Low confidence lysosome-associated membrane glycoprotein 2 precursor (lamp-2) (cd107b antigen). [swissprot;acc:p13473] 2399.5 543.5 4.4149
5 High confidence junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2] 1153.5 339.5 3.39764
Low confidence oxysterol binding protein-related protein 6 (osbp-related protein 6) (orp-6). [swissprot;acc:q9bzf3] 736.5 2113.5 2.86965
6 High confidence junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39] 1153.5 339.5 3.39764
Low confidence oxysterol binding protein-related protein 3 (osbp-related protein 3) (orp-3). [swissprot;acc:q9h4l5] 736.5 2113.5 2.86965
7 High confidence sphingomyelin phosphodiesterase 2 (ec 3.1.4.12) (neutral sphingomyelinase) (nsmase) (n-smase) (lyso-platelet activating factor- phospholipase c) (lyso-paf-plc). [swissprot;acc:o60906] 1153.5 339.5 3.39764
Low confidence oxysterol binding protein-related protein 7 (osbp-related protein 7) (orp-7). [swissprot;acc:q9bzf2] 736.5 2113.5 2.86965
8 High confidence db83 protein. [swissprot;acc:p57088] 1153.5 339.5 3.39764
Low confidence phosphatidylinositol-glycan biosynthesis, class f protein (pig-f). [swissprot;acc:q07326] 3278 5058.5 1.54317
9 High confidence tob2 protein (transducer of erbb-2 2). [swissprot;acc:q14106] 398.5 1281.5 3.21581
Low confidence n33 protein. [swissprot;acc:q13454] 3278 5058.5 1.54317
10 High confidence tob1 protein (transducer of erbb-2 1). [swissprot;acc:p50616] 398.5 1281.5 3.21581
Low confidence implantation-associated protein. [refseq;acc:nm_032121] 3278 5058.5 1.54317
11 High confidence dab2 interacting protein; ngap-like protein; doc-2/dab2 interactive protein. [refseq;acc:nm_032552] 398.5 1281.5 3.21581
Low confidence thyroid receptor interacting protein 8 (trip-8) (fragment). [swissprot;acc:q15652] 1917.64 2950.5 1.53861
12 High confidence cytoplasmic polyadenylation element binding protein 4. [refseq;acc:nm_030627] 398.5 1281.5 3.21581
Low confidence gbp protein isoform a. [refseq;acc:nm_017870] 1921.96 2954.24 1.5371
13 High confidence cytoplasmic polyadenylation element binding protein 3. [refseq;acc:nm_014912] 398.5 1281.5 3.21581
Low confidence jumonji domain containing 1; zinc finger protein; testis-specific protein a. [refseq;acc:nm_018433] 1927.68 2959.19 1.5351
14 High confidence ras gtpase-activating protein ngap (ras protein activator like 1). [swissprot;acc:q9ujf2] 398.5 1281.5 3.21581
Low confidence trypsin iii precursor (ec 3.4.21.4) (brain trypsinogen) (mesotrypsinogen) (trypsin iv). [swissprot;acc:p35030] 1972.65 2998.1 1.51983
15 High confidence xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [refseq;acc:nm_007266] 2671 871 3.06659
Low confidence trypsin i precursor (ec 3.4.21.4) (cationic trypsinogen). [swissprot;acc:p07477] 1983.91 3007.85 1.51612
16 High confidence protein x 0004. [refseq;acc:nm_016301] 2671 871 3.06659
Low confidence 28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5] 21185 28492 1.34491
17 High confidence dgcr14 protein (digeorge syndrome critical region 14) (es2 protein). [swissprot;acc:q96df8] 460 1365 2.96739
Low confidence mitochondrial solute carrier protein. [refseq;acc:nm_145305] 21185 28492 1.34491
18 High confidence protein phosphatase 1, regulatory (inhibitor) subunit 14a; 17-kda pkc-potentiated inhibitory protein of pp1. [refseq;acc:nm_033256] 677.5 1865.5 2.75351
Low confidence cyclic-amp-dependent transcription factor atf-3 (activating transcription factor 3). [swissprot;acc:p18847] 5492.04 7251 1.32027
19 High confidence microfibril-associated glycoprotein 4 precursor. [swissprot;acc:p55083] 677.5 1865.5 2.75351
Low confidence 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] 3032.56 3915.4 1.29112
20 High confidence protein phosphatase 1, regulatory subunit 14d; pkc-dependent pp1 inhibitory protein. [refseq;acc:nm_017726] 677.5 1865.5 2.75351
Low confidence retinoblastoma-associated factor 600. [refseq;acc:nm_020765] 7256.71 9368.87 1.29106
21 High confidence ficolin 2 precursor (collagen/fibrinogen domain-containing protein 2) (ficolin-b) (ficolin b) (serum lectin p35) (ebp-37) (hucolin) (l- ficolin). [swissprot;acc:q15485] 677.5 1865.5 2.75351
Low confidence 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
22 High confidence protein phosphatase 1, regulatory (inhibitor) subunit 14c; serologically defined breast cancer antigen ny-br-81; pkc-potentiated pp1 inhibitory protein. [refseq;acc:nm_030949] 677.5 1865.5 2.75351
Low confidence 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] 3126.88 3997.02 1.27828
23 High confidence gbp protein isoform a. [refseq;acc:nm_017870] 699.76 1894.39 2.7072
Low confidence carboxypeptidase d precursor (ec 3.4.17.-) (gp180). [swissprot;acc:o75976] 40899 32028.5 1.27696
24 High confidence protein kinase, interferon-inducible double stranded rna dependent activator; protein activator of the interferon-induced protein kinase. [refseq;acc:nm_003690] 950.561 2108.52 2.21818
Low confidence atlastin; guanylate-binding protein 3. [refseq;acc:nm_015915] 5720.25 4577.5 1.24965
25 High confidence guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-7 subunit. [swissprot;acc:o60262] 1833.01 892.67 2.0534
Low confidence 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] 5847.46 4691.96 1.24627

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/