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 [...,...].
Filtered Rank Gene Value Type green description Network Comparison Type Interaction Map network_comparison red
Results: HTML CSV LaTeX Showing element 1 to 50 of 12912 in total
Filtered  : 1
Network Comparison Type  : Divided
Interaction Map  : High confidence
Rank
Value Type
green
description
network_comparison
red
1 Measured 2394.5 rad50-interacting protein 1. [refseq;acc:nm_021930] 5.31521 450.5
Ranked 24 putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172] 2.4 10
Squared 1357.07 rad50-interacting protein 1. [refseq;acc:nm_021930] 28.2513 48.0356
Rooted 48.9336 2.30547 21.225
2 Measured 2394.5 rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6] 5.31521 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
Squared 1357.07 rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6] 28.2513 48.0356
Rooted 48.9336 2.30547 21.225
3 Measured 698.5 homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774] 3.71868 2597.5
Ranked 28 cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438] 1.86667 15
Squared 115.48 homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774] 13.8285 1596.92
Rooted 26.4292 1.92839 50.9657
4 Measured 698.5 hbs1-like. [refseq;acc:nm_006620] 3.71868 2597.5
Ranked 28 cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418] 1.86667 15
Squared 115.48 hbs1-like. [refseq;acc:nm_006620] 13.8285 1596.92
Rooted 26.4292 1.92839 50.9657
5 Measured 339.5 junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2] 3.39764 1153.5
Ranked 28 cytohesin 4. [swissprot;acc:q9uia0] 1.86667 15
Squared 27.2805 junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2] 11.544 314.926
Rooted 18.4255 1.84327 33.9632
6 Measured 339.5 junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39] 3.39764 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
Squared 27.2805 junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39] 11.544 314.926
Rooted 18.4255 1.84327 33.9632
7 Measured 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 1153.5
Ranked 322 homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774] 1.49767 215
Squared 27.2805 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] 11.544 314.926
Rooted 18.4255 1.84327 33.9632
8 Measured 339.5 db83 protein. [swissprot;acc:p57088] 3.39764 1153.5
Ranked 322 hbs1-like. [refseq;acc:nm_006620] 1.49767 215
Squared 27.2805 db83 protein. [swissprot;acc:p57088] 11.544 314.926
Rooted 18.4255 1.84327 33.9632
9 Measured 1281.5 tob2 protein (transducer of erbb-2 2). [swissprot;acc:q14106] 3.21581 398.5
Ranked 309 xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [refseq;acc:nm_007266] 1.45755 212
Squared 388.696 tob2 protein (transducer of erbb-2 2). [swissprot;acc:q14106] 10.3414 37.5863
Rooted 35.798 1.79326 19.9625
10 Measured 1281.5 tob1 protein (transducer of erbb-2 1). [swissprot;acc:p50616] 3.21581 398.5
Ranked 309 protein x 0004. [refseq;acc:nm_016301] 1.45755 212
Squared 388.696 tob1 protein (transducer of erbb-2 1). [swissprot;acc:p50616] 10.3414 37.5863
Rooted 35.798 1.79326 19.9625
11 Measured 1281.5 dab2 interacting protein; ngap-like protein; doc-2/dab2 interactive protein. [refseq;acc:nm_032552] 3.21581 398.5
Ranked 232 rad50-interacting protein 1. [refseq;acc:nm_021930] 1.45259 337
Squared 388.696 dab2 interacting protein; ngap-like protein; doc-2/dab2 interactive protein. [refseq;acc:nm_032552] 10.3414 37.5863
Rooted 35.798 1.79326 19.9625
12 Measured 1281.5 cytoplasmic polyadenylation element binding protein 4. [refseq;acc:nm_030627] 3.21581 398.5
Ranked 232 rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6] 1.45259 337
Squared 388.696 cytoplasmic polyadenylation element binding protein 4. [refseq;acc:nm_030627] 10.3414 37.5863
Rooted 35.798 1.79326 19.9625
13 Measured 1281.5 cytoplasmic polyadenylation element binding protein 3. [refseq;acc:nm_014912] 3.21581 398.5
Ranked 212.554 protein cgi-126 (protein hspc155). [swissprot;acc:q9y3c8] 1.3585 288.754

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/