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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Gene Rank Filtered Value Type Network Comparison Type description Interaction Map green red network_comparison
Results: HTML CSV LaTeX Showing element 1 to 50 of 19268 in total
Value Type  : Ranked
Rank
Filtered
Network Comparison Type
description
Interaction Map
green
red
network_comparison
1 0 Divided adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61] High confidence 15915 4294 3.70633
mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849] Low confidence 14977 5865 2.55362
Subtracted mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3] High confidence 21883 8906 12977
Low confidence
1 Divided carboxypeptidase d precursor (ec 3.4.17.-) (gp180). [swissprot;acc:o75976] 32 16 2
putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172] High confidence 24 10 2.4
Subtracted homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774] 322 215 107
lysosome-associated membrane glycoprotein 1 precursor (lamp-1) (cd107a antigen). [swissprot;acc:p11279] Low confidence 330 223
2 0 Divided mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3] 21883 8906 2.45711
mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849] High confidence 14977 5865 2.55362
Subtracted adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61] 15915 4294 11621
neurogenic locus notch homolog protein 1 precursor (notch 1) (hn1) (translocation-associated notch protein tan-1). [swissprot;acc:p46531] Low confidence 20617 9607 11010
1 Divided lysosome-associated membrane glycoprotein 1 precursor (lamp-1) (cd107a antigen). [swissprot;acc:p11279] 330 223 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] High confidence 28 15 1.86667
Subtracted cell division protein kinase 4 (ec 2.7.1.37) (cyclin-dependent kinase 4) (psk-j3). [swissprot;acc:p11802] Low confidence 330 223 107
hbs1-like. [refseq;acc:nm_006620] High confidence 322 215
3 0 Divided neurogenic locus notch homolog protein 1 precursor (notch 1) (hn1) (translocation-associated notch protein tan-1). [swissprot;acc:p46531] Low confidence 20617 9607 2.14604
nif3-like protein 1 (amyotrophic lateral sclerosis 2 chromosomal region candidate gene protein 1) (my018 protein) (mds015). [swissprot;acc:q9gzt8] High confidence 11083.9 4475.84 2.47638
Subtracted cab2. [refseq;acc:nm_033419] 10950 21866 10916
neurogenic locus notch homolog protein 2 precursor (notch 2) (hn2). [swissprot;acc:q04721] Low confidence 20617 9607 11010
1 Divided cell division protein kinase 4 (ec 2.7.1.37) (cyclin-dependent kinase 4) (psk-j3). [swissprot;acc:p11802] 330 223 1.47982
cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438] High confidence 28 15 1.86667
Subtracted cell division protein kinase 6 (ec 2.7.1.37) (serine/threonine protein kinase plstire). [swissprot;acc:q00534] Low confidence 330 223 107
rad50-interacting protein 1. [refseq;acc:nm_021930] High confidence 232 337 105
4 0 Divided mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3] 21883 8906 2.45711
neurogenic locus notch homolog protein 2 precursor (notch 2) (hn2). [swissprot;acc:q04721] Low confidence 20617 9607 2.14604
Subtracted mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849] 14977 5865 9112
nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7] High confidence 21888 11525 10363
1 Divided cell division protein kinase 6 (ec 2.7.1.37) (serine/threonine protein kinase plstire). [swissprot;acc:q00534] Low confidence 330 223 1.47982
cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418] High confidence 28 15 1.86667
Subtracted lysosome-associated membrane glycoprotein 2 precursor (lamp-2) (cd107b antigen). [swissprot;acc:p13473] Low confidence 330 223 107
rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6] High confidence 232 337 105
5 0 Divided ubiquitin-like protein smt3b (sentrin 2) (hsmt3). [swissprot;acc:p55855] 11965.7 5510.5 2.17144
ubiquitously transcribed y chromosome tetratricopeptide repeat protein (ubiquitously transcribed tpr protein on the y chromosome). [swissprot;acc:o14607] Low confidence 19873 10889.4 1.82499
Subtracted homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] 13216 22286 9070
transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87] High confidence 21888 11525 10363
1 Divided cytohesin 4. [swissprot;acc:q9uia0] 28 15 1.86667
lysosome-associated membrane glycoprotein 2 precursor (lamp-2) (cd107b antigen). [swissprot;acc:p13473] Low confidence 330 223 1.47982
Subtracted oxysterol binding protein-related protein 6 (osbp-related protein 6) (orp-6). [swissprot;acc:q9bzf3] 240 318 78
xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [refseq;acc:nm_007266] High confidence 309 212 97
6 0 Divided trinucleotide repeat containing 15. [refseq;acc:nm_015575] Low confidence 9583.37 5575.71 1.71877
ubiquitin protein ligase. [refseq;acc:nm_130466] High confidence 15339.2 7523 2.03897
Subtracted homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] Low confidence 13216 22286 9070
mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849] High confidence 14977 5865 9112
1 Divided cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739] 28 15 1.86667
oxysterol binding protein-related protein 6 (osbp-related protein 6) (orp-6). [swissprot;acc:q9bzf3] Low confidence 240 318 1.325
Subtracted oxysterol binding protein-related protein 3 (osbp-related protein 3) (orp-3). [swissprot;acc:q9h4l5] 78
protein x 0004. [refseq;acc:nm_016301] High confidence 309 212 97
7 0 Divided cab2. [refseq;acc:nm_033419] 10950 21866 1.99689
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 6812 11543 1.69451

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/