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 red green network_comparison
Results: HTML CSV LaTeX Showing element 144 to 193 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
Hugo
description
Value Type
red
green
network_comparison
36 PANK1 pantothenate kinase 1 (ec 2.7.1.33) (pantothenic acid kinase 1) (hpank1) (hpank). [swissprot;acc:q8te04] Squared 106226 192141 1.80879
37 GNAT1 guanine nucleotide-binding protein g(t), alpha-1 subunit (transducin alpha-1 chain). [swissprot;acc:p11488] Measured 1836.76 907.763 2.02339
Rooted 40.2805 24.3691 1.65293
PANK2 pantothenate kinase 2, mitochondrial precursor (ec 2.7.1.33) (pantothenic acid kinase 2) (hpank2). [swissprot;acc:q9bz23] Squared 106226 192141 1.80879
PPP1R14A protein phosphatase 1, regulatory (inhibitor) subunit 14a; 17-kda pkc-potentiated inhibitory protein of pp1. [refseq;acc:nm_033256] Ranked 322 253 1.27273
38 GNAT2 guanine nucleotide-binding protein g(t), alpha-2 subunit (transducin alpha-2 chain). [swissprot;acc:p19087] Measured 1836.76 907.774 2.02337
Rooted 40.2804 24.3692 1.65292
MFAP4 microfibril-associated glycoprotein 4 precursor. [swissprot;acc:p55083] Ranked 322 253 1.27273
PANK3 pantothenate kinase 3 (ec 2.7.1.33) (pantothenic acid kinase 3) (hpank3). [swissprot;acc:q9h999] Squared 106226 192141 1.80879
39 GNAI2 guanine nucleotide-binding protein g(i), alpha-2 subunit (adenylate cyclase-inhibiting g alpha protein). [swissprot;acc:p04899] Measured 1836.8 907.903 2.02312
Rooted 40.28 24.37 1.65285
PPP1R14D protein phosphatase 1, regulatory subunit 14d; pkc-dependent pp1 inhibitory protein. [refseq;acc:nm_017726] Ranked 322 253 1.27273
SLC25A43 mitochondrial solute carrier protein. [refseq;acc:nm_145305] Squared 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 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 322 253 1.27273
GNAI1 guanine nucleotide-binding protein g(i), alpha-1 subunit (adenylate cyclase-inhibiting g alpha protein). [swissprot;acc:p04898] Measured 1836.81 907.978 2.02297
Rooted 40.2797 24.3705 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 322 253 1.27273
GNAI3 guanine nucleotide-binding protein g(k), alpha subunit (g(i) alpha-3). [swissprot;acc:p08754] Measured 1836.81 907.978 2.02297
Rooted 40.2797 24.3705 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 144912 81155 1.78562
42 FOS proto-oncogene protein c-fos (cellular oncogene fos) (g0/g1 switch regulatory protein 7). [swissprot;acc:p01100] Ranked 204.641 160.957 1.2714
GNB5 guanine nucleotide-binding protein beta subunit 5 (transducin beta chain 5). [swissprot;acc:o14775] Measured 1857.32 958.237 1.93827
Rooted 40.225 24.7051 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 144911 81154.7 1.78561
43 no value jun dimerization protein. [refseq;acc:nm_130469] Ranked 204.641 160.957 1.2714
ATG4B cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326] Squared 144876 81136.5 1.78558
GNB1 guanine nucleotide-binding protein g(i)/g(s)/g(t) beta subunit 1 (transducin beta chain 1). [swissprot;acc:p04901] Rooted 40.6302 25.4452 1.59677
GNB3 guanine nucleotide-binding protein g(i)/g(s)/g(t) beta subunit 3 (transducin beta chain 3). [swissprot;acc:p16520] Measured 1881.02 1027.36 1.83093
44 FOSL2 fos-related antigen 2. [swissprot;acc:p15408] Ranked 204.641 161.046 1.2707
GABARAP gaba(a) receptor-associated protein; gaba(a)-receptor-associated protein. [refseq;acc:nm_007278] Squared 139741 78454.6 1.78117
GNB1 guanine nucleotide-binding protein g(i)/g(s)/g(t) beta subunit 1 (transducin beta chain 1). [swissprot;acc:p04901] Measured 1931.34 1057.39 1.82652
GNB4 guanine nucleotide-binding protein beta subunit 4 (transducin beta chain 4). [swissprot;acc:q9hav0] Rooted 40.5691 25.4263 1.59556
45 no value gaba-a receptor-associated protein. [sptrembl;acc:q9by60] Squared 129597 73157.5 1.77148
FOSB protein fosb (g0/g1 switch regulatory protein 3). [swissprot;acc:p53539] Ranked 204.641 161.051 1.27066
GNB3 guanine nucleotide-binding protein g(i)/g(s)/g(t) beta subunit 3 (transducin beta chain 3). [swissprot;acc:p16520] Rooted 40.081 25.1546 1.59339
GNB4 guanine nucleotide-binding protein beta subunit 4 (transducin beta chain 4). [swissprot;acc:q9hav0] Measured 1926.69 1056.02 1.82448
46 ATG3 apg3p; pc3-96 protein. [refseq;acc:nm_022488] Squared 129597 73157.5 1.77148
DTX2 deltex 2. [refseq;acc:nm_020892] Rooted 27.634 43.9629 1.5909
FOSL1 fos-related antigen 1 (fra-1). [swissprot;acc:p15407] Ranked 204.642 161.068 1.27053
NEUROD2 neurogenic differentiation factor 2 (neurod2). [swissprot;acc:q15784] Measured 779.167 1390.33 1.78438
47 no value ubiquitin activating enzyme e1-like protein. [refseq;acc:nm_006395] Squared 98517.9 56927.2 1.73059
CHD3 chromodomain helicase-dna-binding protein 3 (chd-3) (mi-2 autoantigen 240 kda protein) (mi2-alpha). [swissprot;acc:q12873] Measured 779.167 1390.33 1.78438
DTX1 deltex homolog 1; hdx-1. [refseq;acc:nm_004416] Rooted 27.7078 44.017 1.58861
TMEM132A gbp protein isoform a. [refseq;acc:nm_017870] Ranked 325.586 256.492 1.26938
48 CDK2AP2 doc-1 related protein (doc-1r). [swissprot;acc:o75956] Measured 779.167 1390.33 1.78438
GABARAP gaba(a) receptor-associated protein; gaba(a)-receptor-associated protein. [refseq;acc:nm_007278] Ranked 65.4586 83.0461 1.26868
LASS2 lag1 longevity assurance homolog 2 isoform 1; l3 pigment; tumor metastasis-suppressor. [refseq;acc:nm_022075] Squared 6300.2 10703.5 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 27.7254 44.0299 1.58807
49 ARRB2 beta-arrestin 2 (arrestin, beta 2). [swissprot;acc:p32121] Ranked 133 105 1.26667

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/