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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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 Filtered Value Type Network Comparison Type Interaction Map description 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
Interaction Map
description
green
red
network_comparison
1 0 Divided High confidence adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61] 15915 4294 3.70633
Low confidence mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849] 14977 5865 2.55362
Subtracted High confidence mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3] 21883 8906 12977
Low confidence
1 Divided 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
Subtracted High confidence homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774] 322 215 107
Low confidence lysosome-associated membrane glycoprotein 1 precursor (lamp-1) (cd107a antigen). [swissprot;acc:p11279] 330 223
2 0 Divided High confidence mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849] 14977 5865 2.55362
Low confidence mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3] 21883 8906 2.45711
Subtracted High confidence adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61] 15915 4294 11621
Low confidence neurogenic locus notch homolog protein 1 precursor (notch 1) (hn1) (translocation-associated notch protein tan-1). [swissprot;acc:p46531] 20617 9607 11010
1 Divided 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
Subtracted High confidence hbs1-like. [refseq;acc:nm_006620] 322 215 107
Low confidence cell division protein kinase 4 (ec 2.7.1.37) (cyclin-dependent kinase 4) (psk-j3). [swissprot;acc:p11802] 330 223
3 0 Divided High confidence nif3-like protein 1 (amyotrophic lateral sclerosis 2 chromosomal region candidate gene protein 1) (my018 protein) (mds015). [swissprot;acc:q9gzt8] 11083.9 4475.84 2.47638
Low confidence neurogenic locus notch homolog protein 1 precursor (notch 1) (hn1) (translocation-associated notch protein tan-1). [swissprot;acc:p46531] 20617 9607 2.14604
Subtracted High confidence cab2. [refseq;acc:nm_033419] 10950 21866 10916
Low confidence neurogenic locus notch homolog protein 2 precursor (notch 2) (hn2). [swissprot;acc:q04721] 20617 9607 11010
1 Divided 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
Subtracted High confidence rad50-interacting protein 1. [refseq;acc:nm_021930] 232 337 105
Low confidence cell division protein kinase 6 (ec 2.7.1.37) (serine/threonine protein kinase plstire). [swissprot;acc:q00534] 330 223 107
4 0 Divided High confidence mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3] 21883 8906 2.45711
Low confidence neurogenic locus notch homolog protein 2 precursor (notch 2) (hn2). [swissprot;acc:q04721] 20617 9607 2.14604
Subtracted High confidence nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7] 21888 11525 10363
Low confidence mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849] 14977 5865 9112
1 Divided 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
Subtracted High confidence rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6] 232 337 105
Low confidence lysosome-associated membrane glycoprotein 2 precursor (lamp-2) (cd107b antigen). [swissprot;acc:p13473] 330 223 107
5 0 Divided High confidence ubiquitin-like protein smt3b (sentrin 2) (hsmt3). [swissprot;acc:p55855] 11965.7 5510.5 2.17144
Low confidence ubiquitously transcribed y chromosome tetratricopeptide repeat protein (ubiquitously transcribed tpr protein on the y chromosome). [swissprot;acc:o14607] 19873 10889.4 1.82499
Subtracted High confidence transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87] 21888 11525 10363
Low confidence homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] 13216 22286 9070
1 Divided 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
Subtracted High confidence xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [refseq;acc:nm_007266] 309 212 97
Low confidence oxysterol binding protein-related protein 6 (osbp-related protein 6) (orp-6). [swissprot;acc:q9bzf3] 240 318 78
6 0 Divided High confidence ubiquitin protein ligase. [refseq;acc:nm_130466] 15339.2 7523 2.03897
Low confidence trinucleotide repeat containing 15. [refseq;acc:nm_015575] 9583.37 5575.71 1.71877
Subtracted High confidence mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849] 14977 5865 9112
Low confidence homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] 13216 22286 9070
1 Divided 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
Subtracted High confidence protein x 0004. [refseq;acc:nm_016301] 309 212 97
Low confidence oxysterol binding protein-related protein 3 (osbp-related protein 3) (orp-3). [swissprot;acc:q9h4l5] 240 318 78
7 0 Divided High confidence cab2. [refseq;acc:nm_033419] 10950 21866 1.99689
Low confidence fatty acid desaturase 1; linoleoyl-coa desaturase (delta-6-desaturase)-like 1; delta-5 desaturase; delta-5 fatty acid desaturase. [refseq;acc:nm_013402] 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/