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 Network Comparison Type description Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 1 to 50 of 6456 in total
Value Type  : Measured
Interaction Map  : High confidence
Filtered  : 1
Rank
Network Comparison Type
description
red
green
network_comparison
1 Divided rad50-interacting protein 1. [refseq;acc:nm_021930] 450.5 2394.5 5.31521
Subtracted 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] 41482.5 33356.5 8126
2 Divided rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6] 450.5 2394.5 5.31521
Subtracted cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438] 41482.5 33356.5 8126
3 Divided homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774] 2597.5 698.5 3.71868
Subtracted cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418] 41482.5 33356.5 8126
4 Divided hbs1-like. [refseq;acc:nm_006620] 2597.5 698.5 3.71868
Subtracted cytohesin 4. [swissprot;acc:q9uia0] 41482.5 33356.5 8126
5 Divided junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2] 1153.5 339.5 3.39764
Subtracted cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739] 41482.5 33356.5 8126
6 Divided junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39] 1153.5 339.5 3.39764
Subtracted putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172] 44490.5 36927.5 7563
7 Divided 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] 1153.5 339.5 3.39764
Subtracted 28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5] 21185 28492 7307
8 Divided db83 protein. [swissprot;acc:p57088] 1153.5 339.5 3.39764
Subtracted pantothenate kinase 1 (ec 2.7.1.33) (pantothenic acid kinase 1) (hpank1) (hpank). [swissprot;acc:q8te04] 21185 28492 7307
9 Divided tob2 protein (transducer of erbb-2 2). [swissprot;acc:q14106] 398.5 1281.5 3.21581
Subtracted pantothenate kinase 2, mitochondrial precursor (ec 2.7.1.33) (pantothenic acid kinase 2) (hpank2). [swissprot;acc:q9bz23] 21185 28492 7307
10 Divided tob1 protein (transducer of erbb-2 1). [swissprot;acc:p50616] 398.5 1281.5 3.21581
Subtracted pantothenate kinase 3 (ec 2.7.1.33) (pantothenic acid kinase 3) (hpank3). [swissprot;acc:q9h999] 21185 28492 7307
11 Divided dab2 interacting protein; ngap-like protein; doc-2/dab2 interactive protein. [refseq;acc:nm_032552] 398.5 1281.5 3.21581
Subtracted mitochondrial solute carrier protein. [refseq;acc:nm_145305] 21185 28492 7307
12 Divided cytoplasmic polyadenylation element binding protein 4. [refseq;acc:nm_030627] 398.5 1281.5 3.21581
Subtracted nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333] 34190.9 40795.8 6604.9
13 Divided cytoplasmic polyadenylation element binding protein 3. [refseq;acc:nm_014912] 398.5 1281.5 3.21581
Subtracted myosin vb (myosin 5b) (fragment). [swissprot;acc:q9ulv0] 21591.5 27904.5 6313
14 Divided ras gtpase-activating protein ngap (ras protein activator like 1). [swissprot;acc:q9ujf2] 398.5 1281.5 3.21581
Subtracted myosin vc (myosin 5c). [swissprot;acc:q9nqx4] 21591.5 27904.5 6313
15 Divided xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [refseq;acc:nm_007266] 2671 871 3.06659
Subtracted myosin va (myosin 5a) (dilute myosin heavy chain, non-muscle) (myosin heavy chain 12) (myoxin). [swissprot;acc:q9y4i1] 21591.5 27904.5 6313
16 Divided protein x 0004. [refseq;acc:nm_016301] 2671 871 3.06659
Subtracted cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936] 24260.3 18172.1 6088.2
17 Divided dgcr14 protein (digeorge syndrome critical region 14) (es2 protein). [swissprot;acc:q96df8] 460 1365 2.96739
Subtracted microtubule-associated proteins 1a/1b light chain 3b (map1a/map1b lc3 b) (map1a/1b light chain 3 b). [swissprot;acc:q9gzq8] 24255.7 18168.9 6086.8
18 Divided protein phosphatase 1, regulatory (inhibitor) subunit 14a; 17-kda pkc-potentiated inhibitory protein of pp1. [refseq;acc:nm_033256] 677.5 1865.5 2.75351
Subtracted microtubule-associated proteins 1a/1b light chain 3a (map1a/map1b lc3 a) (map1a/1b light chain 3 a). [swissprot;acc:q9h492] 24255.7 18168.9 6086.8
19 Divided microfibril-associated glycoprotein 4 precursor. [swissprot;acc:p55083] 677.5 1865.5 2.75351
Subtracted cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326] 24250 18164.9 6085.1
20 Divided protein phosphatase 1, regulatory subunit 14d; pkc-dependent pp1 inhibitory protein. [refseq;acc:nm_017726] 677.5 1865.5 2.75351
Subtracted gaba(a) receptor-associated protein; gaba(a)-receptor-associated protein. [refseq;acc:nm_007278] 23421.5 17580.4 5841.1
21 Divided ficolin 2 precursor (collagen/fibrinogen domain-containing protein 2) (ficolin-b) (ficolin b) (serum lectin p35) (ebp-37) (hucolin) (l- ficolin). [swissprot;acc:q15485] 677.5 1865.5 2.75351
Subtracted melanoma antigen, family d, 4 isoform 1; mage1 protein; mage-e1 protein; maged4 protein. [refseq;acc:nm_030801] 23693.7 18263 5430.7
22 Divided protein phosphatase 1, regulatory (inhibitor) subunit 14c; serologically defined breast cancer antigen ny-br-81; pkc-potentiated pp1 inhibitory protein. [refseq;acc:nm_030949] 677.5 1865.5 2.75351
Subtracted hepatocellular carcinoma-associated protein hca3. [refseq;acc:nm_138703] 23693.7 18263 5430.7
23 Divided gbp protein isoform a. [refseq;acc:nm_017870] 699.76 1894.39 2.7072
Subtracted melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [swissprot;acc:p43357] 23693.7 18263 5430.7
24 Divided protein kinase, interferon-inducible double stranded rna dependent activator; protein activator of the interferon-induced protein kinase. [refseq;acc:nm_003690] 950.561 2108.52 2.21818
Subtracted melanoma-associated antigen 11 (mage-11 antigen). [swissprot;acc:p43364] 23693.7 18263 5430.7
25 Divided guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-7 subunit. [swissprot;acc:o60262] 1833.01 892.67 2.0534
Subtracted melanoma-associated antigen 2 (mage-2 antigen). [swissprot;acc:p43356] 23693.7 18263 5430.7

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/