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.


Navigation/Query Panel:
Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].
Rank Gene Hugo Value Type description Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 144 to 193 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
Hugo
Value Type
description
Network Comparison Type
red
green
network_comparison
18 PSCD2 Rooted cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418] Subtracted 203.673 182.638 21.035
19 no value Ranked guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 like subunit. [swissprot;acc:q9y3k8] 266.865 336.178 69.313
ATG4B Measured cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326] 24250 18164.9 6085.1
MAGEF1 Squared melanoma-associated antigen f1 (mage-f1 antigen). [swissprot;acc:q9hay2] 219048 129762 89286
MFAP4 Measured microfibril-associated glycoprotein 4 precursor. [swissprot;acc:p55083] Divided 677.5 1865.5 2.75351
Squared 108.641 823.69 7.58176
PRKRAP1 Rooted protein kinase, interferon-inducible double stranded rna dependent activator; protein activator of the interferon-induced protein kinase. [refseq;acc:nm_003690] 25.6987 43.561 1.69507
PSCD4 cytohesin 4. [swissprot;acc:q9uia0] Subtracted 203.673 182.638 21.035
PYGB Ranked glycogen phosphorylase, brain form (ec 2.4.1.1). [swissprot;acc:p11216] Divided 185.678 245.247 1.32082
20 no value Rooted guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-7 subunit. [swissprot;acc:o60262] 40.3337 24.2744 1.66157
GABARAP Measured gaba(a) receptor-associated protein; gaba(a)-receptor-associated protein. [refseq;acc:nm_007278] Subtracted 23421.5 17580.4 5841.1
GNG11 Ranked guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-11 subunit. [swissprot;acc:p50152] 266.868 336.159 69.291
MAGEB6B Squared melanoma antigen, family b, 6. [refseq;acc:nm_173523] 219048 129762 89286
PPP1R14D Measured protein phosphatase 1, regulatory subunit 14d; pkc-dependent pp1 inhibitory protein. [refseq;acc:nm_017726] Divided 677.5 1865.5 2.75351
Squared 108.641 823.69 7.58176
PSCD3 Rooted cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739] Subtracted 203.673 182.638 21.035
PYGL Ranked glycogen phosphorylase, liver form (ec 2.4.1.1). [swissprot;acc:p06737] Divided 185.678 245.247 1.32082
21 no value Squared melanoma-associated antigen 4 (mage-4 antigen) (mage-x2) (mage-41). [swissprot;acc:p43358] Subtracted 219048 129762 89286
ATG4A Rooted cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936] 153.602 133.195 20.407
FCN2 Measured ficolin 2 precursor (collagen/fibrinogen domain-containing protein 2) (ficolin-b) (ficolin b) (serum lectin p35) (ebp-37) (hucolin) (l- ficolin). [swissprot;acc:q15485] Divided 677.5 1865.5 2.75351
Squared 108.641 823.69 7.58176
GNG12 Rooted guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-12 subunit. [swissprot;acc:q9ubi6] 40.3337 24.2744 1.66157
MAGED4 Measured melanoma antigen, family d, 4 isoform 1; mage1 protein; mage-e1 protein; maged4 protein. [refseq;acc:nm_030801] Subtracted 23693.7 18263 5430.7
MYO15A Ranked myosin xv (unconventional myosin-15). [swissprot;acc:q9ukn7] Divided 185.678 245.247 1.32082
TMEM132A gbp protein isoform a. [refseq;acc:nm_017870] Subtracted 325.586 256.492 69.094
22 no value Measured protein phosphatase 1, regulatory (inhibitor) subunit 14c; serologically defined breast cancer antigen ny-br-81; pkc-potentiated pp1 inhibitory protein. [refseq;acc:nm_030949] Divided 677.5 1865.5 2.75351
Squared 108.641 823.69 7.58176
GNG4 Rooted guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-4 subunit. [swissprot;acc:p50150] 40.3357 24.2915 1.66049
MAGEA9 Squared melanoma-associated antigen 9 (mage-9 antigen). [swissprot;acc:p43362] Subtracted 219048 129762 89286
MAGEE2 Measured hepatocellular carcinoma-associated protein hca3. [refseq;acc:nm_138703] 23693.7 18263 5430.7
MAP1LC3B Rooted microtubule-associated proteins 1a/1b light chain 3b (map1a/map1b lc3 b) (map1a/1b light chain 3 b). [swissprot;acc:q9gzq8] 153.578 133.176 20.402
PPP1R14A Ranked protein phosphatase 1, regulatory (inhibitor) subunit 14a; 17-kda pkc-potentiated inhibitory protein of pp1. [refseq;acc:nm_033256] 322 253 69
PYGM glycogen phosphorylase, muscle form (ec 2.4.1.1) (myophosphorylase). [swissprot;acc:p11217] Divided 185.678 245.247 1.32082
23 no value Measured melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [swissprot;acc:p43357] Subtracted 23693.7 18263 5430.7
GNG3 Rooted guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-3 subunit. [swissprot;acc:p29798] Divided 40.3358 24.2919 1.66046
MAGEA8 Squared melanoma-associated antigen 8 (mage-8 antigen). [swissprot;acc:p43361] Subtracted 219048 129762 89286
MAP1LC3A Rooted microtubule-associated proteins 1a/1b light chain 3a (map1a/map1b lc3 a) (map1a/1b light chain 3 a). [swissprot;acc:q9h492] 153.578 133.176 20.402
MFAP4 Ranked microfibril-associated glycoprotein 4 precursor. [swissprot;acc:p55083] 322 253 69
MRPS17 28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5] Divided 58 44 1.31818
NEUROD2 Squared neurogenic differentiation factor 2 (neurod2). [swissprot;acc:q15784] 143.692 457.521 3.18404
TMEM132A Measured gbp protein isoform a. [refseq;acc:nm_017870] 699.76 1894.39 2.7072
24 ATG4B Rooted cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326] Subtracted 153.548 133.153 20.395
CHD3 Squared chromodomain helicase-dna-binding protein 3 (chd-3) (mi-2 autoantigen 240 kda protein) (mi2-alpha). [swissprot;acc:q12873] Divided 143.692 457.521 3.18404
GNG8 Rooted guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-8 subunit (gamma-9). [swissprot;acc:q9uk08] 40.336 24.2941 1.66032
MAGEA11 Measured melanoma-associated antigen 11 (mage-11 antigen). [swissprot;acc:p43364] Subtracted 23693.7 18263 5430.7
MAGEC1 Squared melanoma-associated antigen c1 (mage-c1 antigen) (cancer-testis antigen ct7). [swissprot;acc:o60732] 219048 129762 89286
PANK1 Ranked pantothenate kinase 1 (ec 2.7.1.33) (pantothenic acid kinase 1) (hpank1) (hpank). [swissprot;acc:q8te04] Divided 58 44 1.31818
PPP1R14D protein phosphatase 1, regulatory subunit 14d; pkc-dependent pp1 inhibitory protein. [refseq;acc:nm_017726] Subtracted 322 253 69
PRKRAP1 Measured protein kinase, interferon-inducible double stranded rna dependent activator; protein activator of the interferon-induced protein kinase. [refseq;acc:nm_003690] Divided 950.561 2108.52 2.21818
25 no value guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-7 subunit. [swissprot;acc:o60262] 1833.01 892.67 2.0534

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/