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 - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.


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Rank Gene description Network Comparison Type Hugo Value Type Interaction Map Filtered red network_comparison green
Results: HTML CSV LaTeX Showing element 1 to 50 of 16578 in total
Value Type  : Ranked
Filtered  : 1
Rank
description
Network Comparison Type
Hugo
Interaction Map
red
network_comparison
green
1 carboxypeptidase d precursor (ec 3.4.17.-) (gp180). [swissprot;acc:o75976] Divided CPD Low confidence 16 2 32
homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774] Subtracted HLX High confidence 215 107 322
lysosome-associated membrane glycoprotein 1 precursor (lamp-1) (cd107a antigen). [swissprot;acc:p11279] LAMP1 Low confidence 223 330
putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172] Divided UBAC1 High confidence 10 2.4 24
2 cell division protein kinase 4 (ec 2.7.1.37) (cyclin-dependent kinase 4) (psk-j3). [swissprot;acc:p11802] Subtracted CDK4 Low confidence 223 107 330
hbs1-like. [refseq;acc:nm_006620] HBS1L High confidence 215 322
lysosome-associated membrane glycoprotein 1 precursor (lamp-1) (cd107a antigen). [swissprot;acc:p11279] Divided LAMP1 Low confidence 223 1.47982 330
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] no value High confidence 15 1.86667 28
3 cell division protein kinase 4 (ec 2.7.1.37) (cyclin-dependent kinase 4) (psk-j3). [swissprot;acc:p11802] CDK4 Low confidence 223 1.47982 330
cell division protein kinase 6 (ec 2.7.1.37) (serine/threonine protein kinase plstire). [swissprot;acc:q00534] Subtracted CDK6 107
cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438] Divided PSCD1 High confidence 15 1.86667 28
rad50-interacting protein 1. [refseq;acc:nm_021930] Subtracted RINT1 337 105 232
4 cell division protein kinase 6 (ec 2.7.1.37) (serine/threonine protein kinase plstire). [swissprot;acc:q00534] Divided CDK6 Low confidence 223 1.47982 330
cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418] PSCD2 High confidence 15 1.86667 28
lysosome-associated membrane glycoprotein 2 precursor (lamp-2) (cd107b antigen). [swissprot;acc:p13473] Subtracted LAMP2 Low confidence 223 107 330
rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6] RHOBTB2 High confidence 337 105 232
5 cytohesin 4. [swissprot;acc:q9uia0] Divided PSCD4 15 1.86667 28
lysosome-associated membrane glycoprotein 2 precursor (lamp-2) (cd107b antigen). [swissprot;acc:p13473] LAMP2 Low confidence 223 1.47982 330
oxysterol binding protein-related protein 6 (osbp-related protein 6) (orp-6). [swissprot;acc:q9bzf3] Subtracted OSBPL6 318 78 240
xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [refseq;acc:nm_007266] XAB1 High confidence 212 97 309
6 cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739] Divided PSCD3 15 1.86667 28
oxysterol binding protein-related protein 3 (osbp-related protein 3) (orp-3). [swissprot;acc:q9h4l5] Subtracted OSBPL3 Low confidence 318 78 240
oxysterol binding protein-related protein 6 (osbp-related protein 6) (orp-6). [swissprot;acc:q9bzf3] Divided OSBPL6 1.325
protein x 0004. [refseq;acc:nm_016301] Subtracted ATPBD1C High confidence 212 97 309
7 homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774] Divided HLX 215 1.49767 322
oxysterol binding protein-related protein 3 (osbp-related protein 3) (orp-3). [swissprot;acc:q9h4l5] OSBPL3 Low confidence 318 1.325 240
oxysterol binding protein-related protein 7 (osbp-related protein 7) (orp-7). [swissprot;acc:q9bzf2] Subtracted OSBPL7 78
protein cgi-126 (protein hspc155). [swissprot;acc:q9y3c8] UFC1 High confidence 288.754 76.2 212.554
8 hbs1-like. [refseq;acc:nm_006620] Divided HBS1L 215 1.49767 322
junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2] Subtracted JPH3 288 74 362
oxysterol binding protein-related protein 7 (osbp-related protein 7) (orp-7). [swissprot;acc:q9bzf2] Divided OSBPL7 Low confidence 318 1.325 240
thyroid receptor interacting protein 8 (trip-8) (fragment). [swissprot;acc:q15652] Subtracted JMJD1C 305.472 58.226 247.246
9 28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5] Divided MRPS17 58 1.31818 44
gbp protein isoform a. [refseq;acc:nm_017870] Subtracted TMEM132A 305.399 58.186 247.213
junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39] JPH2 High confidence 288 74 362
xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [refseq;acc:nm_007266] Divided XAB1 212 1.45755 309
10 jumonji domain containing 1; zinc finger protein; testis-specific protein a. [refseq;acc:nm_018433] Subtracted JMJD1A Low confidence 305.303 58.134 247.169
mitochondrial solute carrier protein. [refseq;acc:nm_145305] Divided SLC25A43 58 1.31818 44
protein x 0004. [refseq;acc:nm_016301] ATPBD1C High confidence 212 1.45755 309
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] Subtracted SMPD2 288 74 362
11 bestrophin (vitelliform macular dystrophy protein) (tu15b). [swissprot;acc:o76090] Divided BEST1 Low confidence 37.318 1.30966 28.4944
db83 protein. [swissprot;acc:p57088] Subtracted TMEM33 High confidence 288 74 362
rad50-interacting protein 1. [refseq;acc:nm_021930] Divided RINT1 337 1.45259 232
trypsin iii precursor (ec 3.4.21.4) (brain trypsinogen) (mesotrypsinogen) (trypsin iv). [swissprot;acc:p35030] Subtracted PRSS3 Low confidence 304.548 57.724 246.824
12 guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-7 subunit. [swissprot;acc:o60262] no value High confidence 266.856 69.377 336.233
rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6] Divided RHOBTB2 337 1.45259 232
trypsin i precursor (ec 3.4.21.4) (cationic trypsinogen). [swissprot;acc:p07477] Subtracted PRSS1 Low confidence 304.359 57.622 246.737
vitelliform macular dystrophy 2-like protein 2. [refseq;acc:nm_153274] Divided BEST4 37.3475 1.30933 28.5242
13 guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-12 subunit. [swissprot;acc:q9ubi6] Subtracted GNG12 High confidence 266.856 69.377 336.233
nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333] Divided no value Low confidence 37.9984 1.30207 29.1831

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/