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 - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.


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