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 description Filtered Value Type Interaction Map Network Comparison Type network_comparison green red
Results: HTML CSV LaTeX Showing element 1 to 50 of 9634 in total
Value Type  : Ranked
Network Comparison Type  : Divided
Rank
description
Filtered
Interaction Map
network_comparison
green
red
1 adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61] 0 High confidence 3.70633 15915 4294
carboxypeptidase d precursor (ec 3.4.17.-) (gp180). [swissprot;acc:o75976] 1 Low confidence 2 32 16
mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849] 0 2.55362 14977 5865
putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172] 1 High confidence 2.4 24 10
2 lysosome-associated membrane glycoprotein 1 precursor (lamp-1) (cd107a antigen). [swissprot;acc:p11279] Low confidence 1.47982 330 223
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 1.86667 28 15
mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3] 0 Low confidence 2.45711 21883 8906
mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849] High confidence 2.55362 14977 5865
3 cell division protein kinase 4 (ec 2.7.1.37) (cyclin-dependent kinase 4) (psk-j3). [swissprot;acc:p11802] 1 Low confidence 1.47982 330 223
cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438] High confidence 1.86667 28 15
neurogenic locus notch homolog protein 1 precursor (notch 1) (hn1) (translocation-associated notch protein tan-1). [swissprot;acc:p46531] 0 Low confidence 2.14604 20617 9607
nif3-like protein 1 (amyotrophic lateral sclerosis 2 chromosomal region candidate gene protein 1) (my018 protein) (mds015). [swissprot;acc:q9gzt8] High confidence 2.47638 11083.9 4475.84
4 cell division protein kinase 6 (ec 2.7.1.37) (serine/threonine protein kinase plstire). [swissprot;acc:q00534] 1 Low confidence 1.47982 330 223
cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418] High confidence 1.86667 28 15
mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3] 0 2.45711 21883 8906
neurogenic locus notch homolog protein 2 precursor (notch 2) (hn2). [swissprot;acc:q04721] Low confidence 2.14604 20617 9607
5 cytohesin 4. [swissprot;acc:q9uia0] 1 High confidence 1.86667 28 15
lysosome-associated membrane glycoprotein 2 precursor (lamp-2) (cd107b antigen). [swissprot;acc:p13473] Low confidence 1.47982 330 223
ubiquitin-like protein smt3b (sentrin 2) (hsmt3). [swissprot;acc:p55855] 0 High confidence 2.17144 11965.7 5510.5
ubiquitously transcribed y chromosome tetratricopeptide repeat protein (ubiquitously transcribed tpr protein on the y chromosome). [swissprot;acc:o14607] Low confidence 1.82499 19873 10889.4
6 cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739] 1 High confidence 1.86667 28 15
oxysterol binding protein-related protein 6 (osbp-related protein 6) (orp-6). [swissprot;acc:q9bzf3] Low confidence 1.325 240 318
trinucleotide repeat containing 15. [refseq;acc:nm_015575] 0 1.71877 9583.37 5575.71
ubiquitin protein ligase. [refseq;acc:nm_130466] High confidence 2.03897 15339.2 7523
7 cab2. [refseq;acc:nm_033419] 1.99689 10950 21866
fatty acid desaturase 1; linoleoyl-coa desaturase (delta-6-desaturase)-like 1; delta-5 desaturase; delta-5 fatty acid desaturase. [refseq;acc:nm_013402] Low confidence 1.69451 6812 11543
homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774] 1 High confidence 1.49767 322 215
oxysterol binding protein-related protein 3 (osbp-related protein 3) (orp-3). [swissprot;acc:q9h4l5] Low confidence 1.325 240 318
8 hbs1-like. [refseq;acc:nm_006620] High confidence 1.49767 322 215
homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] 0 Low confidence 1.68629 13216 22286
nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7] High confidence 1.89918 21888 11525
oxysterol binding protein-related protein 7 (osbp-related protein 7) (orp-7). [swissprot;acc:q9bzf2] 1 Low confidence 1.325 240 318
9 28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5] 1.31818 44 58
homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] 0 1.68629 13216 22286
transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87] High confidence 1.89918 21888 11525
xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [refseq;acc:nm_007266] 1 1.45755 309 212
10 fructose-1,6-bisphosphatase isozyme 2 (ec 3.1.3.11) (d-fructose-1,6- bisphosphate 1-phosphohydrolase) (fbpase). [swissprot;acc:o00757] 0 1.88805 14178.1 7509.39
homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056] Low confidence 1.68629 13216 22286
mitochondrial solute carrier protein. [refseq;acc:nm_145305] 1 1.31818 44 58
protein x 0004. [refseq;acc:nm_016301] High confidence 1.45755 309 212
11 ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5] 0 Low confidence 1.66289 8257 13730.5
bestrophin (vitelliform macular dystrophy protein) (tu15b). [swissprot;acc:o76090] 1 1.30966 28.4944 37.318
potential phospholipid-transporting atpase iia (ec 3.6.1.-). [swissprot;acc:o75110] 0 High confidence 1.86092 6248 11627
rad50-interacting protein 1. [refseq;acc:nm_021930] 1 1.45259 232 337
12 anchor attachment protein 1; glycophosphatidylinositol anchor attachment 1; anchor attachment protein 1 (gaa1p, yeast) homolog. [refseq;acc:nm_003801] 0 Low confidence 1.65028 1933 3190
folylpolyglutamate synthase, mitochondrial precursor (ec 6.3.2.17) (folylpoly-gamma-glutamate synthetase) (fpgs). [swissprot;acc:q05932] High confidence 1.81023 5208.84 9429.18
rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6] 1 1.45259 232 337
vitelliform macular dystrophy 2-like protein 2. [refseq;acc:nm_153274] Low confidence 1.30933 28.5242 37.3475
13 heat shock 70 kda protein 1 (hsp70.1) (hsp70-1/hsp70-2). [swissprot;acc:p08107] 0 High confidence 1.77804 9264.5 5210.5
nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333] 1 Low confidence 1.30207 29.1831 37.9984

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/