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 Hugo description Value Type Network Comparison Type Interaction Map Filtered green red network_comparison
Results: HTML CSV LaTeX Showing element 151 to 200 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
Hugo
description
Value Type
green
red
network_comparison
38 MFAP4 microfibril-associated glycoprotein 4 precursor. [swissprot;acc:p55083] Ranked 253 322 1.27273
PANK3 pantothenate kinase 3 (ec 2.7.1.33) (pantothenic acid kinase 3) (hpank3). [swissprot;acc:q9h999] Squared 192141 106226 1.80879
39 GNAI2 guanine nucleotide-binding protein g(i), alpha-2 subunit (adenylate cyclase-inhibiting g alpha protein). [swissprot;acc:p04899] Measured 907.903 1836.8 2.02312
Rooted 24.37 40.28 1.65285
PPP1R14D protein phosphatase 1, regulatory subunit 14d; pkc-dependent pp1 inhibitory protein. [refseq;acc:nm_017726] Ranked 253 322 1.27273
SLC25A43 mitochondrial solute carrier protein. [refseq;acc:nm_145305] Squared 192141 106226 1.80879
40 ATG4A cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936] 81169.7 144940 1.78564
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] Ranked 253 322 1.27273
GNAI1 guanine nucleotide-binding protein g(i), alpha-1 subunit (adenylate cyclase-inhibiting g alpha protein). [swissprot;acc:p04898] Measured 907.978 1836.81 2.02297
Rooted 24.3705 40.2797 1.65281
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] Ranked 253 322 1.27273
GNAI3 guanine nucleotide-binding protein g(k), alpha subunit (g(i) alpha-3). [swissprot;acc:p08754] Measured 907.978 1836.81 2.02297
Rooted 24.3705 40.2797 1.65281
MAP1LC3B microtubule-associated proteins 1a/1b light chain 3b (map1a/map1b lc3 b) (map1a/1b light chain 3 b). [swissprot;acc:q9gzq8] Squared 81155 144912 1.78562
42 FOS proto-oncogene protein c-fos (cellular oncogene fos) (g0/g1 switch regulatory protein 7). [swissprot;acc:p01100] Ranked 160.957 204.641 1.2714
GNB5 guanine nucleotide-binding protein beta subunit 5 (transducin beta chain 5). [swissprot;acc:o14775] Measured 958.237 1857.32 1.93827
Rooted 24.7051 40.225 1.62821
MAP1LC3A microtubule-associated proteins 1a/1b light chain 3a (map1a/map1b lc3 a) (map1a/1b light chain 3 a). [swissprot;acc:q9h492] Squared 81154.7 144911 1.78561
43 no value jun dimerization protein. [refseq;acc:nm_130469] Ranked 160.957 204.641 1.2714
ATG4B cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326] Squared 81136.5 144876 1.78558
GNB1 guanine nucleotide-binding protein g(i)/g(s)/g(t) beta subunit 1 (transducin beta chain 1). [swissprot;acc:p04901] Rooted 25.4452 40.6302 1.59677
GNB3 guanine nucleotide-binding protein g(i)/g(s)/g(t) beta subunit 3 (transducin beta chain 3). [swissprot;acc:p16520] Measured 1027.36 1881.02 1.83093
44 FOSL2 fos-related antigen 2. [swissprot;acc:p15408] Ranked 161.046 204.641 1.2707
GABARAP gaba(a) receptor-associated protein; gaba(a)-receptor-associated protein. [refseq;acc:nm_007278] Squared 78454.6 139741 1.78117
GNB1 guanine nucleotide-binding protein g(i)/g(s)/g(t) beta subunit 1 (transducin beta chain 1). [swissprot;acc:p04901] Measured 1057.39 1931.34 1.82652
GNB4 guanine nucleotide-binding protein beta subunit 4 (transducin beta chain 4). [swissprot;acc:q9hav0] Rooted 25.4263 40.5691 1.59556
45 no value gaba-a receptor-associated protein. [sptrembl;acc:q9by60] Squared 73157.5 129597 1.77148
FOSB protein fosb (g0/g1 switch regulatory protein 3). [swissprot;acc:p53539] Ranked 161.051 204.641 1.27066
GNB3 guanine nucleotide-binding protein g(i)/g(s)/g(t) beta subunit 3 (transducin beta chain 3). [swissprot;acc:p16520] Rooted 25.1546 40.081 1.59339
GNB4 guanine nucleotide-binding protein beta subunit 4 (transducin beta chain 4). [swissprot;acc:q9hav0] Measured 1056.02 1926.69 1.82448
46 ATG3 apg3p; pc3-96 protein. [refseq;acc:nm_022488] Squared 73157.5 129597 1.77148
DTX2 deltex 2. [refseq;acc:nm_020892] Rooted 43.9629 27.634 1.5909
FOSL1 fos-related antigen 1 (fra-1). [swissprot;acc:p15407] Ranked 161.068 204.642 1.27053
NEUROD2 neurogenic differentiation factor 2 (neurod2). [swissprot;acc:q15784] Measured 1390.33 779.167 1.78438
47 no value ubiquitin activating enzyme e1-like protein. [refseq;acc:nm_006395] Squared 56927.2 98517.9 1.73059
CHD3 chromodomain helicase-dna-binding protein 3 (chd-3) (mi-2 autoantigen 240 kda protein) (mi2-alpha). [swissprot;acc:q12873] Measured 1390.33 779.167 1.78438
DTX1 deltex homolog 1; hdx-1. [refseq;acc:nm_004416] Rooted 44.017 27.7078 1.58861
TMEM132A gbp protein isoform a. [refseq;acc:nm_017870] Ranked 256.492 325.586 1.26938
48 CDK2AP2 doc-1 related protein (doc-1r). [swissprot;acc:o75956] Measured 1390.33 779.167 1.78438
GABARAP gaba(a) receptor-associated protein; gaba(a)-receptor-associated protein. [refseq;acc:nm_007278] Ranked 83.0461 65.4586 1.26868
LASS2 lag1 longevity assurance homolog 2 isoform 1; l3 pigment; tumor metastasis-suppressor. [refseq;acc:nm_022075] Squared 10703.5 6300.2 1.69891
PBK t-lak cell-originated protein kinase; spermatogenesis-related protein kinase; pdz-binding kinase; pbk; mapkk-like protein kinase; serine/threonine protein kinase. [refseq;acc:nm_018492] Rooted 44.0299 27.7254 1.58807
49 ARRB2 beta-arrestin 2 (arrestin, beta 2). [swissprot;acc:p32121] Ranked 105 133 1.26667
KHDRBS3 kh domain containing, rna binding, signal transduction associated 3; sam68-like phosphotyrosine protein, t-star. [refseq;acc:nm_006558] Rooted 44.0299 27.7254 1.58807
NEUROD6 neurogenic differentiation factor 6 (neurod6) (my051 protein). [swissprot;acc:q96nk8] Measured 1390.33 779.167 1.78438
STAMBPL1 associated molecule with the sh3 domain of stam (amsh) like protein. [refseq;acc:nm_020799] Squared 17134.8 28994.2 1.69212
50 ARRB1 beta-arrestin 1 (arrestin, beta 1). [swissprot;acc:p49407] Ranked 105 133 1.26667
CHMP2A putative breast adenocarcinoma marker (32kd). [refseq;acc:nm_014453] Squared 17134.8 28994.2 1.69212
KHDRBS1 kh domain containing, rna binding, signal transduction associated 1; gap-associated tyrosine phosphoprotein p62 (sam68). [refseq;acc:nm_006559] Rooted 44.0299 27.7254 1.58807
NEUROD1 neurogenic differentiation factor 1 (neurod1) (neurod). [swissprot;acc:q13562] Measured 1390.33 779.167 1.78438

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/