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 Value Type description Network Comparison Type Interaction Map Filtered red green 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
Value Type
description
red
green
network_comparison
38 MFAP4 Ranked microfibril-associated glycoprotein 4 precursor. [swissprot;acc:p55083] 322 253 1.27273
PANK3 Squared pantothenate kinase 3 (ec 2.7.1.33) (pantothenic acid kinase 3) (hpank3). [swissprot;acc:q9h999] 106226 192141 1.80879
39 GNAI2 Measured guanine nucleotide-binding protein g(i), alpha-2 subunit (adenylate cyclase-inhibiting g alpha protein). [swissprot;acc:p04899] 1836.8 907.903 2.02312
Rooted 40.28 24.37 1.65285
PPP1R14D Ranked protein phosphatase 1, regulatory subunit 14d; pkc-dependent pp1 inhibitory protein. [refseq;acc:nm_017726] 322 253 1.27273
SLC25A43 Squared mitochondrial solute carrier protein. [refseq;acc:nm_145305] 106226 192141 1.80879
40 ATG4A cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936] 144940 81169.7 1.78564
FCN2 Ranked ficolin 2 precursor (collagen/fibrinogen domain-containing protein 2) (ficolin-b) (ficolin b) (serum lectin p35) (ebp-37) (hucolin) (l- ficolin). [swissprot;acc:q15485] 322 253 1.27273
GNAI1 Measured guanine nucleotide-binding protein g(i), alpha-1 subunit (adenylate cyclase-inhibiting g alpha protein). [swissprot;acc:p04898] 1836.81 907.978 2.02297
Rooted 40.2797 24.3705 1.65281
41 no value Ranked protein phosphatase 1, regulatory (inhibitor) subunit 14c; serologically defined breast cancer antigen ny-br-81; pkc-potentiated pp1 inhibitory protein. [refseq;acc:nm_030949] 322 253 1.27273
GNAI3 Measured guanine nucleotide-binding protein g(k), alpha subunit (g(i) alpha-3). [swissprot;acc:p08754] 1836.81 907.978 2.02297
Rooted 40.2797 24.3705 1.65281
MAP1LC3B Squared microtubule-associated proteins 1a/1b light chain 3b (map1a/map1b lc3 b) (map1a/1b light chain 3 b). [swissprot;acc:q9gzq8] 144912 81155 1.78562
42 FOS Ranked proto-oncogene protein c-fos (cellular oncogene fos) (g0/g1 switch regulatory protein 7). [swissprot;acc:p01100] 204.641 160.957 1.2714
GNB5 Measured guanine nucleotide-binding protein beta subunit 5 (transducin beta chain 5). [swissprot;acc:o14775] 1857.32 958.237 1.93827
Rooted 40.225 24.7051 1.62821
MAP1LC3A Squared microtubule-associated proteins 1a/1b light chain 3a (map1a/map1b lc3 a) (map1a/1b light chain 3 a). [swissprot;acc:q9h492] 144911 81154.7 1.78561
43 no value Ranked jun dimerization protein. [refseq;acc:nm_130469] 204.641 160.957 1.2714
ATG4B Squared cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326] 144876 81136.5 1.78558
GNB1 Rooted guanine nucleotide-binding protein g(i)/g(s)/g(t) beta subunit 1 (transducin beta chain 1). [swissprot;acc:p04901] 40.6302 25.4452 1.59677
GNB3 Measured guanine nucleotide-binding protein g(i)/g(s)/g(t) beta subunit 3 (transducin beta chain 3). [swissprot;acc:p16520] 1881.02 1027.36 1.83093
44 FOSL2 Ranked fos-related antigen 2. [swissprot;acc:p15408] 204.641 161.046 1.2707
GABARAP Squared gaba(a) receptor-associated protein; gaba(a)-receptor-associated protein. [refseq;acc:nm_007278] 139741 78454.6 1.78117
GNB1 Measured guanine nucleotide-binding protein g(i)/g(s)/g(t) beta subunit 1 (transducin beta chain 1). [swissprot;acc:p04901] 1931.34 1057.39 1.82652
GNB4 Rooted guanine nucleotide-binding protein beta subunit 4 (transducin beta chain 4). [swissprot;acc:q9hav0] 40.5691 25.4263 1.59556
45 no value Squared gaba-a receptor-associated protein. [sptrembl;acc:q9by60] 129597 73157.5 1.77148
FOSB Ranked protein fosb (g0/g1 switch regulatory protein 3). [swissprot;acc:p53539] 204.641 161.051 1.27066
GNB3 Rooted guanine nucleotide-binding protein g(i)/g(s)/g(t) beta subunit 3 (transducin beta chain 3). [swissprot;acc:p16520] 40.081 25.1546 1.59339
GNB4 Measured guanine nucleotide-binding protein beta subunit 4 (transducin beta chain 4). [swissprot;acc:q9hav0] 1926.69 1056.02 1.82448
46 ATG3 Squared apg3p; pc3-96 protein. [refseq;acc:nm_022488] 129597 73157.5 1.77148
DTX2 Rooted deltex 2. [refseq;acc:nm_020892] 27.634 43.9629 1.5909
FOSL1 Ranked fos-related antigen 1 (fra-1). [swissprot;acc:p15407] 204.642 161.068 1.27053
NEUROD2 Measured neurogenic differentiation factor 2 (neurod2). [swissprot;acc:q15784] 779.167 1390.33 1.78438
47 no value Squared ubiquitin activating enzyme e1-like protein. [refseq;acc:nm_006395] 98517.9 56927.2 1.73059
CHD3 Measured chromodomain helicase-dna-binding protein 3 (chd-3) (mi-2 autoantigen 240 kda protein) (mi2-alpha). [swissprot;acc:q12873] 779.167 1390.33 1.78438
DTX1 Rooted deltex homolog 1; hdx-1. [refseq;acc:nm_004416] 27.7078 44.017 1.58861
TMEM132A Ranked gbp protein isoform a. [refseq;acc:nm_017870] 325.586 256.492 1.26938
48 CDK2AP2 Measured doc-1 related protein (doc-1r). [swissprot;acc:o75956] 779.167 1390.33 1.78438
GABARAP Ranked gaba(a) receptor-associated protein; gaba(a)-receptor-associated protein. [refseq;acc:nm_007278] 65.4586 83.0461 1.26868
LASS2 Squared lag1 longevity assurance homolog 2 isoform 1; l3 pigment; tumor metastasis-suppressor. [refseq;acc:nm_022075] 6300.2 10703.5 1.69891
PBK Rooted 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] 27.7254 44.0299 1.58807
49 ARRB2 Ranked beta-arrestin 2 (arrestin, beta 2). [swissprot;acc:p32121] 133 105 1.26667
KHDRBS3 Rooted kh domain containing, rna binding, signal transduction associated 3; sam68-like phosphotyrosine protein, t-star. [refseq;acc:nm_006558] 27.7254 44.0299 1.58807
NEUROD6 Measured neurogenic differentiation factor 6 (neurod6) (my051 protein). [swissprot;acc:q96nk8] 779.167 1390.33 1.78438
STAMBPL1 Squared associated molecule with the sh3 domain of stam (amsh) like protein. [refseq;acc:nm_020799] 28994.2 17134.8 1.69212
50 ARRB1 Ranked beta-arrestin 1 (arrestin, beta 1). [swissprot;acc:p49407] 133 105 1.26667
CHMP2A Squared putative breast adenocarcinoma marker (32kd). [refseq;acc:nm_014453] 28994.2 17134.8 1.69212
KHDRBS1 Rooted kh domain containing, rna binding, signal transduction associated 1; gap-associated tyrosine phosphoprotein p62 (sam68). [refseq;acc:nm_006559] 27.7254 44.0299 1.58807
NEUROD1 Measured neurogenic differentiation factor 1 (neurod1) (neurod). [swissprot;acc:q13562] 779.167 1390.33 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/