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