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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Rank Value Type Filtered Gene description green Interaction Map Network Comparison Type network_comparison red
Results: HTML CSV LaTeX Showing element 1 to 50 of 14920 in total
Interaction Map  : High confidence
Network Comparison Type  : Divided
Rank
Value Type
Filtered
description
green
network_comparison
red
1 Measured 0 mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3] 0.00001 36400000 364
1 rad50-interacting protein 1. [refseq;acc:nm_021930] 2394.5 5.31521 450.5
Ranked 0 adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61] 15915 3.70633 4294
1 putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172] 24 2.4 10
Squared 0 cab2. [refseq;acc:nm_033419] 7.16592 716592 0.00001
1 rad50-interacting protein 1. [refseq;acc:nm_021930] 1357.07 28.2513 48.0356
Rooted 0 mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3] 0.00001 1907880 19.0788
1 rad50-interacting protein 1. [refseq;acc:nm_021930] 48.9336 2.30547 21.225
2 Measured 0 cab2. [refseq;acc:nm_033419] 174 17400000 0.00001
1 rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6] 2394.5 5.31521 450.5
Ranked 0 mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849] 14977 2.55362 5865
1 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 1.86667 15
Squared 0 nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7] 0.00001 561325 5.61325
1 rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6] 1357.07 28.2513 48.0356
Rooted 0 nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7] 0.00001 1240970 12.4097
1 rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6] 48.9336 2.30547 21.225
3 Measured 0 pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129] 109 10900000 0.00001
1 homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774] 698.5 3.71868 2597.5
Ranked 0 nif3-like protein 1 (amyotrophic lateral sclerosis 2 chromosomal region candidate gene protein 1) (my018 protein) (mds015). [swissprot;acc:q9gzt8] 11083.9 2.47638 4475.84
1 cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438] 28 1.86667 15
Squared 0 transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87] 0.00001 561325 5.61325
1 homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774] 115.48 13.8285 1596.92
Rooted 0 transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87] 0.00001 1240970 12.4097
1 homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774] 26.4292 1.92839 50.9657
4 Measured 0 homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] 89 8900000 0.00001
1 hbs1-like. [refseq;acc:nm_006620] 698.5 3.71868 2597.5
Ranked 0 mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3] 21883 2.45711 8906
1 cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418] 28 1.86667 15
Squared 0 pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129] 2.81207 281207 0.00001
1 hbs1-like. [refseq;acc:nm_006620] 115.48 13.8285 1596.92
Rooted 0 pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129] 10.4403 1044030 0.00001
1 hbs1-like. [refseq;acc:nm_006620] 26.4292 1.92839 50.9657
5 Measured 0 homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] 89 8900000 0.00001
1 junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2] 339.5 3.39764 1153.5
Ranked 0 ubiquitin-like protein smt3b (sentrin 2) (hsmt3). [swissprot;acc:p55855] 11965.7 2.17144 5510.5
1 cytohesin 4. [swissprot;acc:q9uia0] 28 1.86667 15
Squared 0 homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] 1.87479 187479 0.00001
1 junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2] 27.2805 11.544 314.926
Rooted 0 homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] 9.43398 943398 0.00001
1 junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2] 18.4255 1.84327 33.9632
6 Measured 0 homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056] 89 8900000 0.00001
1 junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39] 339.5 3.39764 1153.5
Ranked 0 ubiquitin protein ligase. [refseq;acc:nm_130466] 15339.2 2.03897 7523
1 cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739] 28 1.86667 15
Squared 0 homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] 1.87479 187479 0.00001
1 junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39] 27.2805 11.544 314.926
Rooted 0 homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] 9.43398 943398 0.00001
1 junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39] 18.4255 1.84327 33.9632
7 Measured 0 sedlin. [swissprot;acc:o14582] 43 4300000 0.00001
1 sphingomyelin phosphodiesterase 2 (ec 3.1.4.12) (neutral sphingomyelinase) (nsmase) (n-smase) (lyso-platelet activating factor- phospholipase c) (lyso-paf-plc). [swissprot;acc:o60906] 339.5 3.39764 1153.5

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/