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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Interaction Map Rank Gene Value Type green description network_comparison Filtered Network Comparison Type red
Results: HTML CSV LaTeX Showing element 1 to 50 of 38536 in total
Interaction Map  : High confidence
Network Comparison Type  : Divided
Rank
Value Type
green
description
network_comparison
Filtered
red
1 Measured 0.00001 mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3] 36400000 0 364
2394.5 rad50-interacting protein 1. [refseq;acc:nm_021930] 5.31521 1 450.5
Ranked 24 putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172] 2.4 10
15915 adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61] 3.70633 0 4294
Squared 7.16592 cab2. [refseq;acc:nm_033419] 716592 0.00001
1357.07 rad50-interacting protein 1. [refseq;acc:nm_021930] 28.2513 1 48.0356
Rooted 0.00001 mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3] 1907880 0 19.0788
48.9336 rad50-interacting protein 1. [refseq;acc:nm_021930] 2.30547 1 21.225
2 Measured 174 cab2. [refseq;acc:nm_033419] 17400000 0 0.00001
2394.5 rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6] 5.31521 1 450.5
Ranked 28 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] 1.86667 15
14977 mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849] 2.55362 0 5865
Squared 0.00001 nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7] 561325 5.61325
1357.07 rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6] 28.2513 1 48.0356
Rooted 0.00001 nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7] 1240970 0 12.4097
48.9336 rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6] 2.30547 1 21.225
3 Measured 109 pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129] 10900000 0 0.00001
698.5 homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774] 3.71868 1 2597.5
Ranked 28 cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438] 1.86667 15
11083.9 nif3-like protein 1 (amyotrophic lateral sclerosis 2 chromosomal region candidate gene protein 1) (my018 protein) (mds015). [swissprot;acc:q9gzt8] 2.47638 0 4475.84
Squared 0.00001 transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87] 561325 5.61325
115.48 homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774] 13.8285 1 1596.92
Rooted 0.00001 transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87] 1240970 0 12.4097
26.4292 homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774] 1.92839 1 50.9657
4 Measured 89 homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] 8900000 0 0.00001
698.5 hbs1-like. [refseq;acc:nm_006620] 3.71868 1 2597.5
Ranked 28 cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418] 1.86667 15
21883 mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3] 2.45711 0 8906
Squared 2.81207 pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129] 281207 0.00001
115.48 hbs1-like. [refseq;acc:nm_006620] 13.8285 1 1596.92
Rooted 10.4403 pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129] 1044030 0 0.00001
26.4292 hbs1-like. [refseq;acc:nm_006620] 1.92839 1 50.9657
5 Measured 89 homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] 8900000 0 0.00001
339.5 junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2] 3.39764 1 1153.5
Ranked 28 cytohesin 4. [swissprot;acc:q9uia0] 1.86667 15
11965.7 ubiquitin-like protein smt3b (sentrin 2) (hsmt3). [swissprot;acc:p55855] 2.17144 0 5510.5
Squared 1.87479 homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] 187479 0.00001
27.2805 junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2] 11.544 1 314.926
Rooted 9.43398 homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] 943398 0 0.00001
18.4255 junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2] 1.84327 1 33.9632
6 Measured 89 homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056] 8900000 0 0.00001
339.5 junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39] 3.39764 1 1153.5
Ranked 28 cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739] 1.86667 15
15339.2 ubiquitin protein ligase. [refseq;acc:nm_130466] 2.03897 0 7523
Squared 1.87479 homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] 187479 0.00001
27.2805 junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39] 11.544 1 314.926
Rooted 9.43398 homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] 943398 0 0.00001
18.4255 junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39] 1.84327 1 33.9632
7 Measured 43 sedlin. [swissprot;acc:o14582] 4300000 0 0.00001
339.5 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] 3.39764 1 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/