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

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/