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 red Interaction Map Filtered network_comparison green
Results: HTML CSV LaTeX Showing element 1 to 50 of 6456 in total
Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1
Rank
Network Comparison Type
description
red
network_comparison
green
1 Divided putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172] 10 2.4 24
Subtracted homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774] 215 107 322
2 Divided 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
Subtracted hbs1-like. [refseq;acc:nm_006620] 215 107 322
3 Divided cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438] 15 1.86667 28
Subtracted rad50-interacting protein 1. [refseq;acc:nm_021930] 337 105 232
4 Divided cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418] 15 1.86667 28
Subtracted rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6] 337 105 232
5 Divided cytohesin 4. [swissprot;acc:q9uia0] 15 1.86667 28
Subtracted xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [refseq;acc:nm_007266] 212 97 309
6 Divided cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739] 15 1.86667 28
Subtracted protein x 0004. [refseq;acc:nm_016301] 212 97 309
7 Divided homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774] 215 1.49767 322
Subtracted protein cgi-126 (protein hspc155). [swissprot;acc:q9y3c8] 288.754 76.2 212.554
8 Divided hbs1-like. [refseq;acc:nm_006620] 215 1.49767 322
Subtracted junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2] 288 74 362
9 Divided xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [refseq;acc:nm_007266] 212 1.45755 309
Subtracted junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39] 288 74 362
10 Divided protein x 0004. [refseq;acc:nm_016301] 212 1.45755 309
Subtracted 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] 288 74 362
11 Divided rad50-interacting protein 1. [refseq;acc:nm_021930] 337 1.45259 232
Subtracted db83 protein. [swissprot;acc:p57088] 288 74 362
12 Divided rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6] 337 1.45259 232
Subtracted guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-7 subunit. [swissprot;acc:o60262] 266.856 69.377 336.233
13 Divided protein cgi-126 (protein hspc155). [swissprot;acc:q9y3c8] 288.754 1.3585 212.554
Subtracted guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-12 subunit. [swissprot;acc:q9ubi6] 266.856 69.377 336.233
14 Divided cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936] 56.6768 1.32952 75.3531
Subtracted guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-4 subunit. [swissprot;acc:p50150] 266.863 69.328 336.191
15 Divided microtubule-associated proteins 1a/1b light chain 3b (map1a/map1b lc3 b) (map1a/1b light chain 3 b). [swissprot;acc:q9gzq8] 56.7244 1.32914 75.3948
Subtracted guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-3 subunit. [swissprot;acc:p29798] 266.863 69.327 336.19
16 Divided microtubule-associated proteins 1a/1b light chain 3a (map1a/map1b lc3 a) (map1a/1b light chain 3 a). [swissprot;acc:q9h492] 56.7252 1.32913 75.3954
Subtracted guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-8 subunit (gamma-9). [swissprot;acc:q9uk08] 266.864 69.32 336.184
17 Divided cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326] 56.7841 1.32866 75.447
Subtracted guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 subunit. [swissprot;acc:p30670] 266.864 69.318 336.182
18 Divided 1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446] 185.678 1.32082 245.247
Subtracted guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-10 subunit. [swissprot;acc:p50151] 266.865 69.316 336.181
19 Divided glycogen phosphorylase, brain form (ec 2.4.1.1). [swissprot;acc:p11216] 185.678 1.32082 245.247
Subtracted guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 like subunit. [swissprot;acc:q9y3k8] 266.865 69.313 336.178
20 Divided glycogen phosphorylase, liver form (ec 2.4.1.1). [swissprot;acc:p06737] 185.678 1.32082 245.247
Subtracted guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-11 subunit. [swissprot;acc:p50152] 266.868 69.291 336.159
21 Divided myosin xv (unconventional myosin-15). [swissprot;acc:q9ukn7] 185.678 1.32082 245.247
Subtracted gbp protein isoform a. [refseq;acc:nm_017870] 325.586 69.094 256.492
22 Divided glycogen phosphorylase, muscle form (ec 2.4.1.1) (myophosphorylase). [swissprot;acc:p11217] 185.678 1.32082 245.247
Subtracted protein phosphatase 1, regulatory (inhibitor) subunit 14a; 17-kda pkc-potentiated inhibitory protein of pp1. [refseq;acc:nm_033256] 322 69 253
23 Divided 28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5] 58 1.31818 44
Subtracted microfibril-associated glycoprotein 4 precursor. [swissprot;acc:p55083] 322 69 253
24 Divided pantothenate kinase 1 (ec 2.7.1.33) (pantothenic acid kinase 1) (hpank1) (hpank). [swissprot;acc:q8te04] 58 1.31818 44
Subtracted protein phosphatase 1, regulatory subunit 14d; pkc-dependent pp1 inhibitory protein. [refseq;acc:nm_017726] 322 69 253
25 Divided pantothenate kinase 2, mitochondrial precursor (ec 2.7.1.33) (pantothenic acid kinase 2) (hpank2). [swissprot;acc:q9bz23] 58 1.31818 44
Subtracted ficolin 2 precursor (collagen/fibrinogen domain-containing protein 2) (ficolin-b) (ficolin b) (serum lectin p35) (ebp-37) (hucolin) (l- ficolin). [swissprot;acc:q15485] 322 69 253

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/