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 - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.


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

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/