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

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/