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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Network Comparison Type Rank Value Type Hugo green Gene network_comparison Interaction Map red description Filtered
Results: HTML CSV LaTeX Showing element 1 to 50 of 3228 in total
Network Comparison Type  : Divided
Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1
Rank
Hugo
green
network_comparison
red
description
1 UBAC1 24 2.4 10 putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172]
2 no value 28 1.86667 15 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]
3 PSCD1 cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438]
4 PSCD2 cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418]
5 PSCD4 cytohesin 4. [swissprot;acc:q9uia0]
6 PSCD3 cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739]
7 HLX 322 1.49767 215 homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774]
8 HBS1L hbs1-like. [refseq;acc:nm_006620]
9 XAB1 309 1.45755 212 xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [refseq;acc:nm_007266]
10 ATPBD1C protein x 0004. [refseq;acc:nm_016301]
11 RINT1 232 1.45259 337 rad50-interacting protein 1. [refseq;acc:nm_021930]
12 RHOBTB2 rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6]
13 UFC1 212.554 1.3585 288.754 protein cgi-126 (protein hspc155). [swissprot;acc:q9y3c8]
14 ATG4A 75.3531 1.32952 56.6768 cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936]
15 MAP1LC3B 75.3948 1.32914 56.7244 microtubule-associated proteins 1a/1b light chain 3b (map1a/map1b lc3 b) (map1a/1b light chain 3 b). [swissprot;acc:q9gzq8]
16 MAP1LC3A 75.3954 1.32913 56.7252 microtubule-associated proteins 1a/1b light chain 3a (map1a/map1b lc3 a) (map1a/1b light chain 3 a). [swissprot;acc:q9h492]
17 ATG4B 75.447 1.32866 56.7841 cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326]
18 GBE1 245.247 1.32082 185.678 1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446]
19 PYGB glycogen phosphorylase, brain form (ec 2.4.1.1). [swissprot;acc:p11216]
20 PYGL glycogen phosphorylase, liver form (ec 2.4.1.1). [swissprot;acc:p06737]
21 MYO15A myosin xv (unconventional myosin-15). [swissprot;acc:q9ukn7]
22 PYGM glycogen phosphorylase, muscle form (ec 2.4.1.1) (myophosphorylase). [swissprot;acc:p11217]
23 MRPS17 44 1.31818 58 28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5]
24 PANK1 pantothenate kinase 1 (ec 2.7.1.33) (pantothenic acid kinase 1) (hpank1) (hpank). [swissprot;acc:q8te04]
25 PANK2 pantothenate kinase 2, mitochondrial precursor (ec 2.7.1.33) (pantothenic acid kinase 2) (hpank2). [swissprot;acc:q9bz23]
26 PANK3 pantothenate kinase 3 (ec 2.7.1.33) (pantothenic acid kinase 3) (hpank3). [swissprot;acc:q9h999]
27 SLC25A43 mitochondrial solute carrier protein. [refseq;acc:nm_145305]
28 ATF3 153.671 1.31416 201.949 cyclic-amp-dependent transcription factor atf-3 (activating transcription factor 3). [swissprot;acc:p18847]
29 PPP2R2D 243.678 1.29991 187.458 uncharacterized hematopoietic stem/progenitor cells protein mds026. [sptrembl;acc:q9nz48]
30 no value 187.457 serine/threonine protein phosphatase 2a, 55 kda regulatory subunit b, alpha isoform (pp2a, subunit b, b-alpha isoform) (pp2a, subunit b, b55-alpha isoform) (pp2a, subunit b, pr55-alpha isoform) (pp2a, subunit b, r2-alpha isoform). [swissprot;acc:q00007]
31 PPP2R2B 243.677 1.2999 187.458 serine/threonine protein phosphatase 2a, 55 kda regulatory subunit b, beta isoform (pp2a, subunit b, b-beta isoform) (pp2a, subunit b, b55- beta isoform) (pp2a, subunit b, pr55-beta isoform) (pp2a, subunit b, r2-beta isoform). [swissprot;acc:q00005]
32 PPP2R2C 243.673 1.29985 187.462 serine/threonine protein phosphatase 2a, 55 kda regulatory subunit b, gamma isoform (pp2a, subunit b, b-gamma isoform) (pp2a, subunit b, b55-gamma isoform) (pp2a, subunit b, pr55-gamma isoform) (pp2a, subunit b, r2-gamma isoform) (imypno1). [swissprot;acc:q9y2t4]
33 PPP2R1B 242.742 1.28647 188.688 serine/threonine protein phosphatase 2a, 65 kda regulatory subunit a, beta isoform (pp2a, subunit a, pr65-beta isoform) (pp2a, subunit a, r1-beta isoform). [swissprot;acc:p30154]
34 PPP2R1A 242.453 1.28235 189.07 serine/threonine protein phosphatase 2a, 65 kda regulatory subunit a, alpha isoform (pp2a, subunit a, pr65-alpha isoform) (pp2a, subunit a, r1-alpha isoform) (medium tumor antigen-associated 61 kda protein). [swissprot;acc:p30153]
35 NFYC 204.309 1.27519 260.532 nuclear transcription factor y subunit gamma (nf-y protein chain c) (nuclear factor yc) (nf-yc) (ccaat-binding transcription factor subunit c) (cbf-c) (transactivator hsm-1/2). [swissprot;acc:q13952]
36 NFYA ccaat-binding transcription factor subunit b (cbf-b) (nf-y protein chain a) (nf-ya) (caat-box dna binding protein subunit a). [swissprot;acc:p23511]
37 PPP1R14A 253 1.27273 322 protein phosphatase 1, regulatory (inhibitor) subunit 14a; 17-kda pkc-potentiated inhibitory protein of pp1. [refseq;acc:nm_033256]
38 MFAP4 microfibril-associated glycoprotein 4 precursor. [swissprot;acc:p55083]
39 PPP1R14D protein phosphatase 1, regulatory subunit 14d; pkc-dependent pp1 inhibitory protein. [refseq;acc:nm_017726]
40 FCN2 ficolin 2 precursor (collagen/fibrinogen domain-containing protein 2) (ficolin-b) (ficolin b) (serum lectin p35) (ebp-37) (hucolin) (l- ficolin). [swissprot;acc:q15485]
41 no value protein phosphatase 1, regulatory (inhibitor) subunit 14c; serologically defined breast cancer antigen ny-br-81; pkc-potentiated pp1 inhibitory protein. [refseq;acc:nm_030949]
42 FOS 160.957 1.2714 204.641 proto-oncogene protein c-fos (cellular oncogene fos) (g0/g1 switch regulatory protein 7). [swissprot;acc:p01100]
43 no value jun dimerization protein. [refseq;acc:nm_130469]
44 FOSL2 161.046 1.2707 fos-related antigen 2. [swissprot;acc:p15408]
45 FOSB 161.051 1.27066 protein fosb (g0/g1 switch regulatory protein 3). [swissprot;acc:p53539]
46 FOSL1 161.068 1.27053 204.642 fos-related antigen 1 (fra-1). [swissprot;acc:p15407]
47 TMEM132A 256.492 1.26938 325.586 gbp protein isoform a. [refseq;acc:nm_017870]
48 GABARAP 83.0461 1.26868 65.4586 gaba(a) receptor-associated protein; gaba(a)-receptor-associated protein. [refseq;acc:nm_007278]
49 ARRB2 105 1.26667 133 beta-arrestin 2 (arrestin, beta 2). [swissprot;acc:p32121]
50 ARRB1 beta-arrestin 1 (arrestin, beta 1). [swissprot;acc:p49407]

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
- Hugo is the HGNC identifier if it exists
- 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/