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 Network Comparison Type Hugo description Value Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 1 to 50 of 16578 in total
Value Type  : Ranked
Filtered  : 1
Rank
Network Comparison Type
Hugo
description
Interaction Map
red
green
network_comparison
1 Divided CPD carboxypeptidase d precursor (ec 3.4.17.-) (gp180). [swissprot;acc:o75976] Low confidence 16 32 2
UBAC1 putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172] High confidence 10 24 2.4
Subtracted HLX homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774] 215 322 107
LAMP1 lysosome-associated membrane glycoprotein 1 precursor (lamp-1) (cd107a antigen). [swissprot;acc:p11279] Low confidence 223 330
2 Divided no value mannosyl-oligosaccharide 1,2-alpha-mannosidase ib (ec 3.2.1.113) (processing alpha-1,2-mannosidase ib) (alpha-1,2-mannosidase ib) (mannosidase alpha class 1a member 2). [swissprot;acc:o60476] High confidence 15 28 1.86667
LAMP1 lysosome-associated membrane glycoprotein 1 precursor (lamp-1) (cd107a antigen). [swissprot;acc:p11279] Low confidence 223 330 1.47982
Subtracted CDK4 cell division protein kinase 4 (ec 2.7.1.37) (cyclin-dependent kinase 4) (psk-j3). [swissprot;acc:p11802] 107
HBS1L hbs1-like. [refseq;acc:nm_006620] High confidence 215 322
3 Divided CDK4 cell division protein kinase 4 (ec 2.7.1.37) (cyclin-dependent kinase 4) (psk-j3). [swissprot;acc:p11802] Low confidence 223 330 1.47982
PSCD1 cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438] High confidence 15 28 1.86667
Subtracted CDK6 cell division protein kinase 6 (ec 2.7.1.37) (serine/threonine protein kinase plstire). [swissprot;acc:q00534] Low confidence 223 330 107
RINT1 rad50-interacting protein 1. [refseq;acc:nm_021930] High confidence 337 232 105
4 Divided CDK6 cell division protein kinase 6 (ec 2.7.1.37) (serine/threonine protein kinase plstire). [swissprot;acc:q00534] Low confidence 223 330 1.47982
PSCD2 cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418] High confidence 15 28 1.86667
Subtracted LAMP2 lysosome-associated membrane glycoprotein 2 precursor (lamp-2) (cd107b antigen). [swissprot;acc:p13473] Low confidence 223 330 107
RHOBTB2 rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6] High confidence 337 232 105
5 Divided LAMP2 lysosome-associated membrane glycoprotein 2 precursor (lamp-2) (cd107b antigen). [swissprot;acc:p13473] Low confidence 223 330 1.47982
PSCD4 cytohesin 4. [swissprot;acc:q9uia0] High confidence 15 28 1.86667
Subtracted OSBPL6 oxysterol binding protein-related protein 6 (osbp-related protein 6) (orp-6). [swissprot;acc:q9bzf3] Low confidence 318 240 78
XAB1 xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [refseq;acc:nm_007266] High confidence 212 309 97
6 Divided OSBPL6 oxysterol binding protein-related protein 6 (osbp-related protein 6) (orp-6). [swissprot;acc:q9bzf3] Low confidence 318 240 1.325
PSCD3 cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739] High confidence 15 28 1.86667
Subtracted ATPBD1C protein x 0004. [refseq;acc:nm_016301] 212 309 97
OSBPL3 oxysterol binding protein-related protein 3 (osbp-related protein 3) (orp-3). [swissprot;acc:q9h4l5] Low confidence 318 240 78
7 Divided HLX homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774] High confidence 215 322 1.49767
OSBPL3 oxysterol binding protein-related protein 3 (osbp-related protein 3) (orp-3). [swissprot;acc:q9h4l5] Low confidence 318 240 1.325
Subtracted OSBPL7 oxysterol binding protein-related protein 7 (osbp-related protein 7) (orp-7). [swissprot;acc:q9bzf2] 78
UFC1 protein cgi-126 (protein hspc155). [swissprot;acc:q9y3c8] High confidence 288.754 212.554 76.2
8 Divided HBS1L hbs1-like. [refseq;acc:nm_006620] 215 322 1.49767
OSBPL7 oxysterol binding protein-related protein 7 (osbp-related protein 7) (orp-7). [swissprot;acc:q9bzf2] Low confidence 318 240 1.325
Subtracted JMJD1C thyroid receptor interacting protein 8 (trip-8) (fragment). [swissprot;acc:q15652] 305.472 247.246 58.226
JPH3 junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2] High confidence 288 362 74
9 Divided MRPS17 28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5] Low confidence 58 44 1.31818
XAB1 xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [refseq;acc:nm_007266] High confidence 212 309 1.45755
Subtracted JPH2 junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39] 288 362 74
TMEM132A gbp protein isoform a. [refseq;acc:nm_017870] Low confidence 305.399 247.213 58.186
10 Divided ATPBD1C protein x 0004. [refseq;acc:nm_016301] High confidence 212 309 1.45755
SLC25A43 mitochondrial solute carrier protein. [refseq;acc:nm_145305] Low confidence 58 44 1.31818
Subtracted JMJD1A jumonji domain containing 1; zinc finger protein; testis-specific protein a. [refseq;acc:nm_018433] 305.303 247.169 58.134
SMPD2 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] High confidence 288 362 74
11 Divided BEST1 bestrophin (vitelliform macular dystrophy protein) (tu15b). [swissprot;acc:o76090] Low confidence 37.318 28.4944 1.30966
RINT1 rad50-interacting protein 1. [refseq;acc:nm_021930] High confidence 337 232 1.45259
Subtracted PRSS3 trypsin iii precursor (ec 3.4.21.4) (brain trypsinogen) (mesotrypsinogen) (trypsin iv). [swissprot;acc:p35030] Low confidence 304.548 246.824 57.724
TMEM33 db83 protein. [swissprot;acc:p57088] High confidence 288 362 74
12 Divided BEST4 vitelliform macular dystrophy 2-like protein 2. [refseq;acc:nm_153274] Low confidence 37.3475 28.5242 1.30933
RHOBTB2 rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6] High confidence 337 232 1.45259
Subtracted no value guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-7 subunit. [swissprot;acc:o60262] 266.856 336.233 69.377
PRSS1 trypsin i precursor (ec 3.4.21.4) (cationic trypsinogen). [swissprot;acc:p07477] Low confidence 304.359 246.737 57.622
13 Divided no value nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333] 37.9984 29.1831 1.30207
UFC1 protein cgi-126 (protein hspc155). [swissprot;acc:q9y3c8] High confidence 288.754 212.554 1.3585

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
- Hugo is the HGNC identifier if it exists
- 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/