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 network_comparison green
Results: HTML CSV LaTeX Showing element 151 to 200 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
Hugo
description
Value Type
Network Comparison Type
red
network_comparison
green
19 PSCD4 cytohesin 4. [swissprot;acc:q9uia0] Rooted Subtracted 203.673 21.035 182.638
PYGB glycogen phosphorylase, brain form (ec 2.4.1.1). [swissprot;acc:p11216] Ranked Divided 185.678 1.32082 245.247
20 no value guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-7 subunit. [swissprot;acc:o60262] Rooted 40.3337 1.66157 24.2744
GABARAP gaba(a) receptor-associated protein; gaba(a)-receptor-associated protein. [refseq;acc:nm_007278] Measured Subtracted 23421.5 5841.1 17580.4
GNG11 guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-11 subunit. [swissprot;acc:p50152] Ranked 266.868 69.291 336.159
MAGEB6B melanoma antigen, family b, 6. [refseq;acc:nm_173523] Squared 219048 89286 129762
PPP1R14D protein phosphatase 1, regulatory subunit 14d; pkc-dependent pp1 inhibitory protein. [refseq;acc:nm_017726] Measured Divided 677.5 2.75351 1865.5
Squared 108.641 7.58176 823.69
PSCD3 cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739] Rooted Subtracted 203.673 21.035 182.638
PYGL glycogen phosphorylase, liver form (ec 2.4.1.1). [swissprot;acc:p06737] Ranked Divided 185.678 1.32082 245.247
21 no value melanoma-associated antigen 4 (mage-4 antigen) (mage-x2) (mage-41). [swissprot;acc:p43358] Squared Subtracted 219048 89286 129762
ATG4A cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936] Rooted 153.602 20.407 133.195
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] Measured Divided 677.5 2.75351 1865.5
Squared 108.641 7.58176 823.69
GNG12 guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-12 subunit. [swissprot;acc:q9ubi6] Rooted 40.3337 1.66157 24.2744
MAGED4 melanoma antigen, family d, 4 isoform 1; mage1 protein; mage-e1 protein; maged4 protein. [refseq;acc:nm_030801] Measured Subtracted 23693.7 5430.7 18263
MYO15A myosin xv (unconventional myosin-15). [swissprot;acc:q9ukn7] Ranked Divided 185.678 1.32082 245.247
TMEM132A gbp protein isoform a. [refseq;acc:nm_017870] Subtracted 325.586 69.094 256.492
22 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] Measured Divided 677.5 2.75351 1865.5
Squared 108.641 7.58176 823.69
GNG4 guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-4 subunit. [swissprot;acc:p50150] Rooted 40.3357 1.66049 24.2915
MAGEA9 melanoma-associated antigen 9 (mage-9 antigen). [swissprot;acc:p43362] Squared Subtracted 219048 89286 129762
MAGEE2 hepatocellular carcinoma-associated protein hca3. [refseq;acc:nm_138703] Measured 23693.7 5430.7 18263
MAP1LC3B microtubule-associated proteins 1a/1b light chain 3b (map1a/map1b lc3 b) (map1a/1b light chain 3 b). [swissprot;acc:q9gzq8] Rooted 153.578 20.402 133.176
PPP1R14A protein phosphatase 1, regulatory (inhibitor) subunit 14a; 17-kda pkc-potentiated inhibitory protein of pp1. [refseq;acc:nm_033256] Ranked 322 69 253
PYGM glycogen phosphorylase, muscle form (ec 2.4.1.1) (myophosphorylase). [swissprot;acc:p11217] Divided 185.678 1.32082 245.247
23 no value melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [swissprot;acc:p43357] Measured Subtracted 23693.7 5430.7 18263
GNG3 guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-3 subunit. [swissprot;acc:p29798] Rooted Divided 40.3358 1.66046 24.2919
MAGEA8 melanoma-associated antigen 8 (mage-8 antigen). [swissprot;acc:p43361] Squared Subtracted 219048 89286 129762
MAP1LC3A microtubule-associated proteins 1a/1b light chain 3a (map1a/map1b lc3 a) (map1a/1b light chain 3 a). [swissprot;acc:q9h492] Rooted 153.578 20.402 133.176
MFAP4 microfibril-associated glycoprotein 4 precursor. [swissprot;acc:p55083] Ranked 322 69 253
MRPS17 28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5] Divided 58 1.31818 44
NEUROD2 neurogenic differentiation factor 2 (neurod2). [swissprot;acc:q15784] Squared 143.692 3.18404 457.521
TMEM132A gbp protein isoform a. [refseq;acc:nm_017870] Measured 699.76 2.7072 1894.39
24 ATG4B cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326] Rooted Subtracted 153.548 20.395 133.153
CHD3 chromodomain helicase-dna-binding protein 3 (chd-3) (mi-2 autoantigen 240 kda protein) (mi2-alpha). [swissprot;acc:q12873] Squared Divided 143.692 3.18404 457.521
GNG8 guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-8 subunit (gamma-9). [swissprot;acc:q9uk08] Rooted 40.336 1.66032 24.2941
MAGEA11 melanoma-associated antigen 11 (mage-11 antigen). [swissprot;acc:p43364] Measured Subtracted 23693.7 5430.7 18263
MAGEC1 melanoma-associated antigen c1 (mage-c1 antigen) (cancer-testis antigen ct7). [swissprot;acc:o60732] Squared 219048 89286 129762
PANK1 pantothenate kinase 1 (ec 2.7.1.33) (pantothenic acid kinase 1) (hpank1) (hpank). [swissprot;acc:q8te04] Ranked Divided 58 1.31818 44
PPP1R14D protein phosphatase 1, regulatory subunit 14d; pkc-dependent pp1 inhibitory protein. [refseq;acc:nm_017726] Subtracted 322 69 253
PRKRAP1 protein kinase, interferon-inducible double stranded rna dependent activator; protein activator of the interferon-induced protein kinase. [refseq;acc:nm_003690] Measured Divided 950.561 2.21818 2108.52
25 no value guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-7 subunit. [swissprot;acc:o60262] 1833.01 2.0534 892.67
CDK2AP2 doc-1 related protein (doc-1r). [swissprot;acc:o75956] Squared 143.692 3.18404 457.521
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 Subtracted 322 69 253
GNG5 guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 subunit. [swissprot;acc:p30670] Rooted Divided 40.3361 1.66026 24.295
MAGEA2B melanoma-associated antigen 2 (mage-2 antigen). [swissprot;acc:p43356] Measured Subtracted 23693.7 5430.7 18263
MAGEA4 melanoma-associated antigen 12 (mage-12 antigen) (mage12f). [swissprot;acc:p43365] Squared 219048 89286 129762
MYO5B myosin vb (myosin 5b) (fragment). [swissprot;acc:q9ulv0] Rooted 146.94 20.106 167.046
PANK2 pantothenate kinase 2, mitochondrial precursor (ec 2.7.1.33) (pantothenic acid kinase 2) (hpank2). [swissprot;acc:q9bz23] Ranked Divided 58 1.31818 44

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/