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 red Filtered Interaction Map green network_comparison
Results: HTML CSV LaTeX Showing element 1 to 50 of 19268 in total
Value Type  : Ranked
Rank
description
Network Comparison Type
red
Filtered
Interaction Map
green
network_comparison
1 adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61] Divided 4294 0 High confidence 15915 3.70633
carboxypeptidase d precursor (ec 3.4.17.-) (gp180). [swissprot;acc:o75976] 16 1 Low confidence 32 2
homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774] Subtracted 215 High confidence 322 107
lysosome-associated membrane glycoprotein 1 precursor (lamp-1) (cd107a antigen). [swissprot;acc:p11279] 223 Low confidence 330
mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3] 8906 0 High confidence 21883 12977
Low confidence
mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849] Divided 5865 14977 2.55362
putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172] 10 1 High confidence 24 2.4
2 adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61] Subtracted 4294 0 15915 11621
cell division protein kinase 4 (ec 2.7.1.37) (cyclin-dependent kinase 4) (psk-j3). [swissprot;acc:p11802] 223 1 Low confidence 330 107
hbs1-like. [refseq;acc:nm_006620] 215 High confidence 322
lysosome-associated membrane glycoprotein 1 precursor (lamp-1) (cd107a antigen). [swissprot;acc:p11279] Divided 223 Low confidence 330 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] 15 High confidence 28 1.86667
mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3] 8906 0 Low confidence 21883 2.45711
mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849] 5865 High confidence 14977 2.55362
neurogenic locus notch homolog protein 1 precursor (notch 1) (hn1) (translocation-associated notch protein tan-1). [swissprot;acc:p46531] Subtracted 9607 Low confidence 20617 11010
3 cab2. [refseq;acc:nm_033419] 21866 High confidence 10950 10916
cell division protein kinase 4 (ec 2.7.1.37) (cyclin-dependent kinase 4) (psk-j3). [swissprot;acc:p11802] Divided 223 1 Low confidence 330 1.47982
cell division protein kinase 6 (ec 2.7.1.37) (serine/threonine protein kinase plstire). [swissprot;acc:q00534] Subtracted 107
cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438] Divided 15 High confidence 28 1.86667
neurogenic locus notch homolog protein 1 precursor (notch 1) (hn1) (translocation-associated notch protein tan-1). [swissprot;acc:p46531] 9607 0 Low confidence 20617 2.14604
neurogenic locus notch homolog protein 2 precursor (notch 2) (hn2). [swissprot;acc:q04721] Subtracted 11010
nif3-like protein 1 (amyotrophic lateral sclerosis 2 chromosomal region candidate gene protein 1) (my018 protein) (mds015). [swissprot;acc:q9gzt8] Divided 4475.84 High confidence 11083.9 2.47638
rad50-interacting protein 1. [refseq;acc:nm_021930] Subtracted 337 1 232 105
4 cell division protein kinase 6 (ec 2.7.1.37) (serine/threonine protein kinase plstire). [swissprot;acc:q00534] Divided 223 Low confidence 330 1.47982
cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418] 15 High confidence 28 1.86667
lysosome-associated membrane glycoprotein 2 precursor (lamp-2) (cd107b antigen). [swissprot;acc:p13473] Subtracted 223 Low confidence 330 107
mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3] Divided 8906 0 High confidence 21883 2.45711
mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849] Subtracted 5865 Low confidence 14977 9112
neurogenic locus notch homolog protein 2 precursor (notch 2) (hn2). [swissprot;acc:q04721] Divided 9607 20617 2.14604
nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7] Subtracted 11525 High confidence 21888 10363
rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6] 337 1 232 105
5 cytohesin 4. [swissprot;acc:q9uia0] Divided 15 28 1.86667
homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] Subtracted 22286 0 Low confidence 13216 9070
lysosome-associated membrane glycoprotein 2 precursor (lamp-2) (cd107b antigen). [swissprot;acc:p13473] Divided 223 1 330 1.47982
oxysterol binding protein-related protein 6 (osbp-related protein 6) (orp-6). [swissprot;acc:q9bzf3] Subtracted 318 240 78
transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87] 11525 0 High confidence 21888 10363
ubiquitin-like protein smt3b (sentrin 2) (hsmt3). [swissprot;acc:p55855] Divided 5510.5 11965.7 2.17144
ubiquitously transcribed y chromosome tetratricopeptide repeat protein (ubiquitously transcribed tpr protein on the y chromosome). [swissprot;acc:o14607] 10889.4 Low confidence 19873 1.82499
xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [refseq;acc:nm_007266] Subtracted 212 1 High confidence 309 97
6 cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739] Divided 15 28 1.86667
homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] Subtracted 22286 0 Low confidence 13216 9070
mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849] 5865 High confidence 14977 9112
oxysterol binding protein-related protein 3 (osbp-related protein 3) (orp-3). [swissprot;acc:q9h4l5] 318 1 Low confidence 240 78
oxysterol binding protein-related protein 6 (osbp-related protein 6) (orp-6). [swissprot;acc:q9bzf3] Divided 1.325
protein x 0004. [refseq;acc:nm_016301] Subtracted 212 High confidence 309 97
trinucleotide repeat containing 15. [refseq;acc:nm_015575] Divided 5575.71 0 Low confidence 9583.37 1.71877
ubiquitin protein ligase. [refseq;acc:nm_130466] 7523 High confidence 15339.2 2.03897
7 cab2. [refseq;acc:nm_033419] 21866 10950 1.99689
fatty acid desaturase 1; linoleoyl-coa desaturase (delta-6-desaturase)-like 1; delta-5 desaturase; delta-5 fatty acid desaturase. [refseq;acc:nm_013402] 11543 Low confidence 6812 1.69451

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/