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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Gene Rank Value Type Network Comparison Type green description red Filtered Interaction Map network_comparison
Results: HTML CSV LaTeX Showing element 1 to 50 of 9634 in total
Value Type  : Ranked
Network Comparison Type  : Divided
Rank
green
description
red
Filtered
Interaction Map
network_comparison
1 24 putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172] 10 1 High confidence 2.4
32 carboxypeptidase d precursor (ec 3.4.17.-) (gp180). [swissprot;acc:o75976] 16 Low confidence 2
14977 mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849] 5865 0 2.55362
15915 adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61] 4294 High confidence 3.70633
2 28 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 1 1.86667
330 lysosome-associated membrane glycoprotein 1 precursor (lamp-1) (cd107a antigen). [swissprot;acc:p11279] 223 Low confidence 1.47982
14977 mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849] 5865 0 High confidence 2.55362
21883 mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3] 8906 Low confidence 2.45711
3 28 cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438] 15 1 High confidence 1.86667
330 cell division protein kinase 4 (ec 2.7.1.37) (cyclin-dependent kinase 4) (psk-j3). [swissprot;acc:p11802] 223 Low confidence 1.47982
11083.9 nif3-like protein 1 (amyotrophic lateral sclerosis 2 chromosomal region candidate gene protein 1) (my018 protein) (mds015). [swissprot;acc:q9gzt8] 4475.84 0 High confidence 2.47638
20617 neurogenic locus notch homolog protein 1 precursor (notch 1) (hn1) (translocation-associated notch protein tan-1). [swissprot;acc:p46531] 9607 Low confidence 2.14604
4 28 cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418] 15 1 High confidence 1.86667
330 cell division protein kinase 6 (ec 2.7.1.37) (serine/threonine protein kinase plstire). [swissprot;acc:q00534] 223 Low confidence 1.47982
20617 neurogenic locus notch homolog protein 2 precursor (notch 2) (hn2). [swissprot;acc:q04721] 9607 0 2.14604
21883 mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3] 8906 High confidence 2.45711
5 28 cytohesin 4. [swissprot;acc:q9uia0] 15 1 1.86667
330 lysosome-associated membrane glycoprotein 2 precursor (lamp-2) (cd107b antigen). [swissprot;acc:p13473] 223 Low confidence 1.47982
11965.7 ubiquitin-like protein smt3b (sentrin 2) (hsmt3). [swissprot;acc:p55855] 5510.5 0 High confidence 2.17144
19873 ubiquitously transcribed y chromosome tetratricopeptide repeat protein (ubiquitously transcribed tpr protein on the y chromosome). [swissprot;acc:o14607] 10889.4 Low confidence 1.82499
6 28 cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739] 15 1 High confidence 1.86667
240 oxysterol binding protein-related protein 6 (osbp-related protein 6) (orp-6). [swissprot;acc:q9bzf3] 318 Low confidence 1.325
9583.37 trinucleotide repeat containing 15. [refseq;acc:nm_015575] 5575.71 0 1.71877
15339.2 ubiquitin protein ligase. [refseq;acc:nm_130466] 7523 High confidence 2.03897
7 240 oxysterol binding protein-related protein 3 (osbp-related protein 3) (orp-3). [swissprot;acc:q9h4l5] 318 1 Low confidence 1.325
322 homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774] 215 High confidence 1.49767
6812 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 0 Low confidence 1.69451
10950 cab2. [refseq;acc:nm_033419] 21866 High confidence 1.99689
8 240 oxysterol binding protein-related protein 7 (osbp-related protein 7) (orp-7). [swissprot;acc:q9bzf2] 318 1 Low confidence 1.325
322 hbs1-like. [refseq;acc:nm_006620] 215 High confidence 1.49767
13216 homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] 22286 0 Low confidence 1.68629
21888 nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7] 11525 High confidence 1.89918
9 44 28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5] 58 1 Low confidence 1.31818
309 xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [refseq;acc:nm_007266] 212 High confidence 1.45755
13216 homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] 22286 0 Low confidence 1.68629
21888 transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87] 11525 High confidence 1.89918
10 44 mitochondrial solute carrier protein. [refseq;acc:nm_145305] 58 1 Low confidence 1.31818
309 protein x 0004. [refseq;acc:nm_016301] 212 High confidence 1.45755
13216 homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056] 22286 0 Low confidence 1.68629
14178.1 fructose-1,6-bisphosphatase isozyme 2 (ec 3.1.3.11) (d-fructose-1,6- bisphosphate 1-phosphohydrolase) (fbpase). [swissprot;acc:o00757] 7509.39 High confidence 1.88805
11 28.4944 bestrophin (vitelliform macular dystrophy protein) (tu15b). [swissprot;acc:o76090] 37.318 1 Low confidence 1.30966
232 rad50-interacting protein 1. [refseq;acc:nm_021930] 337 High confidence 1.45259
6248 potential phospholipid-transporting atpase iia (ec 3.6.1.-). [swissprot;acc:o75110] 11627 0 1.86092
8257 ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5] 13730.5 Low confidence 1.66289
12 28.5242 vitelliform macular dystrophy 2-like protein 2. [refseq;acc:nm_153274] 37.3475 1 1.30933
232 rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6] 337 High confidence 1.45259
1933 anchor attachment protein 1; glycophosphatidylinositol anchor attachment 1; anchor attachment protein 1 (gaa1p, yeast) homolog. [refseq;acc:nm_003801] 3190 0 Low confidence 1.65028
5208.84 folylpolyglutamate synthase, mitochondrial precursor (ec 6.3.2.17) (folylpoly-gamma-glutamate synthetase) (fpgs). [swissprot;acc:q05932] 9429.18 High confidence 1.81023
13 29.1831 nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333] 37.9984 1 Low confidence 1.30207
212.554 protein cgi-126 (protein hspc155). [swissprot;acc:q9y3c8] 288.754 High confidence 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
- 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/