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

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/