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.


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