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 Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 1 to 50 of 8289 in total
Value Type  : Ranked
Network Comparison Type  : Divided
Filtered  : 1
Rank
description
Interaction Map
red
green
network_comparison
1 carboxypeptidase d precursor (ec 3.4.17.-) (gp180). [swissprot;acc:o75976] Low confidence 16 32 2
putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172] High confidence 10 24 2.4
2 lysosome-associated membrane glycoprotein 1 precursor (lamp-1) (cd107a antigen). [swissprot;acc:p11279] Low confidence 223 330 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] High confidence 15 28 1.86667
3 cell division protein kinase 4 (ec 2.7.1.37) (cyclin-dependent kinase 4) (psk-j3). [swissprot;acc:p11802] Low confidence 223 330 1.47982
cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438] High confidence 15 28 1.86667
4 cell division protein kinase 6 (ec 2.7.1.37) (serine/threonine protein kinase plstire). [swissprot;acc:q00534] Low confidence 223 330 1.47982
cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418] High confidence 15 28 1.86667
5 cytohesin 4. [swissprot;acc:q9uia0]
lysosome-associated membrane glycoprotein 2 precursor (lamp-2) (cd107b antigen). [swissprot;acc:p13473] Low confidence 223 330 1.47982
6 cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739] High confidence 15 28 1.86667
oxysterol binding protein-related protein 6 (osbp-related protein 6) (orp-6). [swissprot;acc:q9bzf3] Low confidence 318 240 1.325
7 homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774] High confidence 215 322 1.49767
oxysterol binding protein-related protein 3 (osbp-related protein 3) (orp-3). [swissprot;acc:q9h4l5] Low confidence 318 240 1.325
8 hbs1-like. [refseq;acc:nm_006620] High confidence 215 322 1.49767
oxysterol binding protein-related protein 7 (osbp-related protein 7) (orp-7). [swissprot;acc:q9bzf2] Low confidence 318 240 1.325
9 28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5] 58 44 1.31818
xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [refseq;acc:nm_007266] High confidence 212 309 1.45755
10 mitochondrial solute carrier protein. [refseq;acc:nm_145305] Low confidence 58 44 1.31818
protein x 0004. [refseq;acc:nm_016301] High confidence 212 309 1.45755
11 bestrophin (vitelliform macular dystrophy protein) (tu15b). [swissprot;acc:o76090] Low confidence 37.318 28.4944 1.30966
rad50-interacting protein 1. [refseq;acc:nm_021930] High confidence 337 232 1.45259
12 rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6]
vitelliform macular dystrophy 2-like protein 2. [refseq;acc:nm_153274] Low confidence 37.3475 28.5242 1.30933
13 nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333] 37.9984 29.1831 1.30207
protein cgi-126 (protein hspc155). [swissprot;acc:q9y3c8] High confidence 288.754 212.554 1.3585
14 cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936] 56.6768 75.3531 1.32952
vitelliform macular dystrophy 2-like protein 1. [refseq;acc:nm_017682] Low confidence 37.9984 29.1831 1.30207
15 microtubule-associated proteins 1a/1b light chain 3b (map1a/map1b lc3 b) (map1a/1b light chain 3 b). [swissprot;acc:q9gzq8] High confidence 56.7244 75.3948 1.32914
protein cgi-126 (protein hspc155). [swissprot;acc:q9y3c8] Low confidence 255.046 202.362 1.26035
16 microtubule-associated proteins 1a/1b light chain 3a (map1a/map1b lc3 a) (map1a/1b light chain 3 a). [swissprot;acc:q9h492] High confidence 56.7252 75.3954 1.32913
thyroid receptor interacting protein 8 (trip-8) (fragment). [swissprot;acc:q15652] Low confidence 305.472 247.246 1.2355
17 cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326] High confidence 56.7841 75.447 1.32866
gbp protein isoform a. [refseq;acc:nm_017870] Low confidence 305.399 247.213 1.23537
18 1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446] High confidence 185.678 245.247 1.32082
jumonji domain containing 1; zinc finger protein; testis-specific protein a. [refseq;acc:nm_018433] Low confidence 305.303 247.169 1.2352
19 glycogen phosphorylase, brain form (ec 2.4.1.1). [swissprot;acc:p11216] High confidence 185.678 245.247 1.32082
trypsin iii precursor (ec 3.4.21.4) (brain trypsinogen) (mesotrypsinogen) (trypsin iv). [swissprot;acc:p35030] Low confidence 304.548 246.824 1.23387
20 glycogen phosphorylase, liver form (ec 2.4.1.1). [swissprot;acc:p06737] High confidence 185.678 245.247 1.32082
trypsin i precursor (ec 3.4.21.4) (cationic trypsinogen). [swissprot;acc:p07477] Low confidence 304.359 246.737 1.23354
21 myosin xv (unconventional myosin-15). [swissprot;acc:q9ukn7] High confidence 185.678 245.247 1.32082
phosphatidylinositol-glycan biosynthesis, class f protein (pig-f). [swissprot;acc:q07326] Low confidence 198 163 1.21472
22 glycogen phosphorylase, muscle form (ec 2.4.1.1) (myophosphorylase). [swissprot;acc:p11217] High confidence 185.678 245.247 1.32082
n33 protein. [swissprot;acc:q13454] Low confidence 198 163 1.21472
23 28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5] High confidence 58 44 1.31818
implantation-associated protein. [refseq;acc:nm_032121] Low confidence 198 163 1.21472
24 histidine triad nucleotide-binding protein 1 (adenosine 5'- monophosphoramidase) (protein kinase c inhibitor 1) (protein kinase c- interacting protein 1) (pkci-1). [swissprot;acc:p49773] 188.298 228.509 1.21355
pantothenate kinase 1 (ec 2.7.1.33) (pantothenic acid kinase 1) (hpank1) (hpank). [swissprot;acc:q8te04] High confidence 58 44 1.31818
25 25-hydroxyvitamin d-1 alpha hydroxylase, mitochondrial precursor (ec 1.14.-.-) (25-ohd-1 alpha-hydroxylase) (25-hydroxyvitamin d3 1- alpha-hydroxylase) (vd3 1a hydroxylase) (p450c1 alpha) (p450vd1- alpha). [swissprot;acc:o15528] Low confidence 286.396 238.476 1.20094
pantothenate kinase 2, mitochondrial precursor (ec 2.7.1.33) (pantothenic acid kinase 2) (hpank2). [swissprot;acc:q9bz23] High confidence 58 44 1.31818

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/