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