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

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/