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

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/