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.


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Rank Gene Hugo description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 1 to 50 of 9634 in total
Value Type  : Ranked
Network Comparison Type  : Divided
Rank
Hugo
description
Interaction Map
Filtered
red
green
network_comparison
1 ARFGAP3 adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61] High confidence 0 4294 15915 3.70633
CPD carboxypeptidase d precursor (ec 3.4.17.-) (gp180). [swissprot;acc:o75976] Low confidence 1 16 32 2
STARD3 mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849] 0 5865 14977 2.55362
UBAC1 putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172] High confidence 1 10 24 2.4
2 no value 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 28 1.86667
mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3] Low confidence 0 8906 21883 2.45711
LAMP1 lysosome-associated membrane glycoprotein 1 precursor (lamp-1) (cd107a antigen). [swissprot;acc:p11279] 1 223 330 1.47982
STARD3 mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849] High confidence 0 5865 14977 2.55362
3 no value nif3-like protein 1 (amyotrophic lateral sclerosis 2 chromosomal region candidate gene protein 1) (my018 protein) (mds015). [swissprot;acc:q9gzt8] 4475.84 11083.9 2.47638
CDK4 cell division protein kinase 4 (ec 2.7.1.37) (cyclin-dependent kinase 4) (psk-j3). [swissprot;acc:p11802] Low confidence 1 223 330 1.47982
NOTCH1 neurogenic locus notch homolog protein 1 precursor (notch 1) (hn1) (translocation-associated notch protein tan-1). [swissprot;acc:p46531] 0 9607 20617 2.14604
PSCD1 cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438] High confidence 1 15 28 1.86667
4 no value mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3] 0 8906 21883 2.45711
CDK6 cell division protein kinase 6 (ec 2.7.1.37) (serine/threonine protein kinase plstire). [swissprot;acc:q00534] Low confidence 1 223 330 1.47982
NOTCH2 neurogenic locus notch homolog protein 2 precursor (notch 2) (hn2). [swissprot;acc:q04721] 0 9607 20617 2.14604
PSCD2 cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418] High confidence 1 15 28 1.86667
5 no value ubiquitin-like protein smt3b (sentrin 2) (hsmt3). [swissprot;acc:p55855] 0 5510.5 11965.7 2.17144
LAMP2 lysosome-associated membrane glycoprotein 2 precursor (lamp-2) (cd107b antigen). [swissprot;acc:p13473] Low confidence 1 223 330 1.47982
PSCD4 cytohesin 4. [swissprot;acc:q9uia0] High confidence 15 28 1.86667
UTY ubiquitously transcribed y chromosome tetratricopeptide repeat protein (ubiquitously transcribed tpr protein on the y chromosome). [swissprot;acc:o14607] Low confidence 0 10889.4 19873 1.82499
6 no value trinucleotide repeat containing 15. [refseq;acc:nm_015575] 5575.71 9583.37 1.71877
OSBPL6 oxysterol binding protein-related protein 6 (osbp-related protein 6) (orp-6). [swissprot;acc:q9bzf3] 1 318 240 1.325
PSCD3 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
UBE3B ubiquitin protein ligase. [refseq;acc:nm_130466] 0 7523 15339.2 2.03897
7 no value fatty acid desaturase 1; linoleoyl-coa desaturase (delta-6-desaturase)-like 1; delta-5 desaturase; delta-5 fatty acid desaturase. [refseq;acc:nm_013402] Low confidence 11543 6812 1.69451
HLX homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774] High confidence 1 215 322 1.49767
OSBPL3 oxysterol binding protein-related protein 3 (osbp-related protein 3) (orp-3). [swissprot;acc:q9h4l5] Low confidence 318 240 1.325
PERLD1 cab2. [refseq;acc:nm_033419] High confidence 0 21866 10950 1.99689
8 no value homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] Low confidence 22286 13216 1.68629
nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7] High confidence 11525 21888 1.89918
HBS1L hbs1-like. [refseq;acc:nm_006620] 1 215 322 1.49767
OSBPL7 oxysterol binding protein-related protein 7 (osbp-related protein 7) (orp-7). [swissprot;acc:q9bzf2] Low confidence 318 240 1.325
9 no value homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] 0 22286 13216 1.68629
MRPS17 28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5] 1 58 44 1.31818
TBL1Y transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87] High confidence 0 11525 21888 1.89918
XAB1 xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [refseq;acc:nm_007266] 1 212 309 1.45755
10 no value homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056] Low confidence 0 22286 13216 1.68629
ATPBD1C protein x 0004. [refseq;acc:nm_016301] High confidence 1 212 309 1.45755
FBP2 fructose-1,6-bisphosphatase isozyme 2 (ec 3.1.3.11) (d-fructose-1,6- bisphosphate 1-phosphohydrolase) (fbpase). [swissprot;acc:o00757] 0 7509.39 14178.1 1.88805
SLC25A43 mitochondrial solute carrier protein. [refseq;acc:nm_145305] Low confidence 1 58 44 1.31818
11 no value ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5] 0 13730.5 8257 1.66289
ATP9A potential phospholipid-transporting atpase iia (ec 3.6.1.-). [swissprot;acc:o75110] High confidence 11627 6248 1.86092
BEST1 bestrophin (vitelliform macular dystrophy protein) (tu15b). [swissprot;acc:o76090] Low confidence 1 37.318 28.4944 1.30966
RINT1 rad50-interacting protein 1. [refseq;acc:nm_021930] High confidence 337 232 1.45259
12 no value anchor attachment protein 1; glycophosphatidylinositol anchor attachment 1; anchor attachment protein 1 (gaa1p, yeast) homolog. [refseq;acc:nm_003801] Low confidence 0 3190 1933 1.65028
BEST4 vitelliform macular dystrophy 2-like protein 2. [refseq;acc:nm_153274] 1 37.3475 28.5242 1.30933
FPGS folylpolyglutamate synthase, mitochondrial precursor (ec 6.3.2.17) (folylpoly-gamma-glutamate synthetase) (fpgs). [swissprot;acc:q05932] High confidence 0 9429.18 5208.84 1.81023
RHOBTB2 rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6] 1 337 232 1.45259
13 no value heat shock 70 kda protein 1 (hsp70.1) (hsp70-1/hsp70-2). [swissprot;acc:p08107] 0 5210.5 9264.5 1.77804
nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333] Low confidence 1 37.9984 29.1831 1.30207

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
- Hugo is the HGNC identifier if it exists
- 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/