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 1 to 50 of 9634 in total
Value Type  : Measured
Network Comparison Type  : Divided
Rank
description
Interaction Map
Filtered
red
green
network_comparison
1 lysosome-associated membrane glycoprotein 1 precursor (lamp-1) (cd107a antigen). [swissprot;acc:p11279] Low confidence 1 2399.5 543.5 4.4149
mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3] High confidence 0 364 0.00001 36400000
Low confidence
rad50-interacting protein 1. [refseq;acc:nm_021930] High confidence 1 450.5 2394.5 5.31521
2 cab2. [refseq;acc:nm_033419] 0 0.00001 174 17400000
cell division protein kinase 4 (ec 2.7.1.37) (cyclin-dependent kinase 4) (psk-j3). [swissprot;acc:p11802] Low confidence 1 2399.5 543.5 4.4149
homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] 0 0.00001 89 8900000
rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6] High confidence 1 450.5 2394.5 5.31521
3 cell division protein kinase 6 (ec 2.7.1.37) (serine/threonine protein kinase plstire). [swissprot;acc:q00534] Low confidence 2399.5 543.5 4.4149
homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774] High confidence 2597.5 698.5 3.71868
homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] Low confidence 0 0.00001 89 8900000
pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129] High confidence 109 10900000
4 hbs1-like. [refseq;acc:nm_006620] 1 2597.5 698.5 3.71868
homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056] Low confidence 0 0.00001 89 8900000
homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] High confidence
lysosome-associated membrane glycoprotein 2 precursor (lamp-2) (cd107b antigen). [swissprot;acc:p13473] Low confidence 1 2399.5 543.5 4.4149
5 homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] High confidence 0 0.00001 89 8900000
jumonji protein. [swissprot;acc:q92833] Low confidence 17.5166 1751660
junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2] High confidence 1 1153.5 339.5 3.39764
oxysterol binding protein-related protein 6 (osbp-related protein 6) (orp-6). [swissprot;acc:q9bzf3] Low confidence 736.5 2113.5 2.86965
6 homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056] High confidence 0 0.00001 89 8900000
homogentisate 1,2-dioxygenase (ec 1.13.11.5) (homogentisicase) (homogentisate oxygenase) (homogentisic acid oxidase). [swissprot;acc:q93099] Low confidence 13 0.00001 1300000
junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39] High confidence 1 1153.5 339.5 3.39764
oxysterol binding protein-related protein 3 (osbp-related protein 3) (orp-3). [swissprot;acc:q9h4l5] Low confidence 736.5 2113.5 2.86965
7 oxysterol binding protein-related protein 7 (osbp-related protein 7) (orp-7). [swissprot;acc:q9bzf2]
sedlin. [swissprot;acc:o14582] High confidence 0 0.00001 43 4300000
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] 1 1153.5 339.5 3.39764
tbc1 domain family, member 8 (with gram domain); vascular rab-gap/tbc-containing. [refseq;acc:nm_007063] Low confidence 0 2.31962 0.00001 231962
8 ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5] 85 6410 75.4118
db83 protein. [swissprot;acc:p57088] High confidence 1 1153.5 339.5 3.39764
phosphatidylinositol-glycan biosynthesis, class f protein (pig-f). [swissprot;acc:q07326] Low confidence 3278 5058.5 1.54317
synbindin (trs23 homolog) (hematopoietic stem/progenitor cell protein 172) (hspc172) (ptd009) (cgi-104). [swissprot;acc:q9y296] High confidence 0 0.00001 43 4300000
9 ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5] 85 6410 75.4118
n33 protein. [swissprot;acc:q13454] Low confidence 1 3278 5058.5 1.54317
tob2 protein (transducer of erbb-2 2). [swissprot;acc:q14106] High confidence 398.5 1281.5 3.21581
ubiquitously transcribed y chromosome tetratricopeptide repeat protein (ubiquitously transcribed tpr protein on the y chromosome). [swissprot;acc:o14607] Low confidence 0 383.762 10.6048 36.1876
10 implantation-associated protein. [refseq;acc:nm_032121] 1 3278 5058.5 1.54317
lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851] High confidence 0 85 6410 75.4118
serpin b12. [swissprot;acc:q96p63] Low confidence 199.549 5.56738 35.8425
tob1 protein (transducer of erbb-2 1). [swissprot;acc:p50616] High confidence 1 398.5 1281.5 3.21581
11 dab2 interacting protein; ngap-like protein; doc-2/dab2 interactive protein. [refseq;acc:nm_032552]
hurpin (hacat uv-repressible serpin) (protease inhibitor 13) (headpin) (serpin b13). [swissprot;acc:q9uiv8] Low confidence 0 199.249 5.71669 34.8539
serpin b12. [swissprot;acc:q96p63] High confidence 199.549 5.56738 35.8425
thyroid receptor interacting protein 8 (trip-8) (fragment). [swissprot;acc:q15652] Low confidence 1 1917.64 2950.5 1.53861
12 cytoplasmic polyadenylation element binding protein 4. [refseq;acc:nm_030627] High confidence 398.5 1281.5 3.21581
gbp protein isoform a. [refseq;acc:nm_017870] Low confidence 1921.96 2954.24 1.5371
hurpin (hacat uv-repressible serpin) (protease inhibitor 13) (headpin) (serpin b13). [swissprot;acc:q9uiv8] High confidence 0 199.249 5.71669 34.8539
mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849] Low confidence 859 58 14.8103
13 adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61] High confidence 1363 47 29
cytoplasmic polyadenylation element binding protein 3. [refseq;acc:nm_014912] 1 398.5 1281.5 3.21581

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/