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 Network Comparison Type Hugo description Value Type Interaction Map Filtered network_comparison red green
Results: HTML CSV LaTeX Showing element 182 to 231 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
Network Comparison Type
Hugo
description
Value Type
network_comparison
red
green
23 Subtracted MAGEA8 melanoma-associated antigen 8 (mage-8 antigen). [swissprot;acc:p43361] Squared 89286 219048 129762
MAP1LC3A microtubule-associated proteins 1a/1b light chain 3a (map1a/map1b lc3 a) (map1a/1b light chain 3 a). [swissprot;acc:q9h492] Rooted 20.402 153.578 133.176
MFAP4 microfibril-associated glycoprotein 4 precursor. [swissprot;acc:p55083] Ranked 69 322 253
24 Divided CHD3 chromodomain helicase-dna-binding protein 3 (chd-3) (mi-2 autoantigen 240 kda protein) (mi2-alpha). [swissprot;acc:q12873] Squared 3.18404 143.692 457.521
GNG8 guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-8 subunit (gamma-9). [swissprot;acc:q9uk08] Rooted 1.66032 40.336 24.2941
PANK1 pantothenate kinase 1 (ec 2.7.1.33) (pantothenic acid kinase 1) (hpank1) (hpank). [swissprot;acc:q8te04] Ranked 1.31818 58 44
PRKRAP1 protein kinase, interferon-inducible double stranded rna dependent activator; protein activator of the interferon-induced protein kinase. [refseq;acc:nm_003690] Measured 2.21818 950.561 2108.52
Subtracted ATG4B cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326] Rooted 20.395 153.548 133.153
MAGEA11 melanoma-associated antigen 11 (mage-11 antigen). [swissprot;acc:p43364] Measured 5430.7 23693.7 18263
MAGEC1 melanoma-associated antigen c1 (mage-c1 antigen) (cancer-testis antigen ct7). [swissprot;acc:o60732] Squared 89286 219048 129762
PPP1R14D protein phosphatase 1, regulatory subunit 14d; pkc-dependent pp1 inhibitory protein. [refseq;acc:nm_017726] Ranked 69 322 253
25 Divided no value guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-7 subunit. [swissprot;acc:o60262] Measured 2.0534 1833.01 892.67
CDK2AP2 doc-1 related protein (doc-1r). [swissprot;acc:o75956] Squared 3.18404 143.692 457.521
GNG5 guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 subunit. [swissprot;acc:p30670] Rooted 1.66026 40.3361 24.295
PANK2 pantothenate kinase 2, mitochondrial precursor (ec 2.7.1.33) (pantothenic acid kinase 2) (hpank2). [swissprot;acc:q9bz23] Ranked 1.31818 58 44
Subtracted 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] 69 322 253
MAGEA2B melanoma-associated antigen 2 (mage-2 antigen). [swissprot;acc:p43356] Measured 5430.7 23693.7 18263
MAGEA4 melanoma-associated antigen 12 (mage-12 antigen) (mage12f). [swissprot;acc:p43365] Squared 89286 219048 129762
MYO5B myosin vb (myosin 5b) (fragment). [swissprot;acc:q9ulv0] Rooted 20.106 146.94 167.046
26 Divided GNG10 guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-10 subunit. [swissprot;acc:p50151] 1.66024 40.3362 24.2954
GNG12 guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-12 subunit. [swissprot;acc:q9ubi6] Measured 2.0534 1833.01 892.67
NEUROD6 neurogenic differentiation factor 6 (neurod6) (my051 protein). [swissprot;acc:q96nk8] Squared 3.18404 143.692 457.521
PANK3 pantothenate kinase 3 (ec 2.7.1.33) (pantothenic acid kinase 3) (hpank3). [swissprot;acc:q9h999] Ranked 1.31818 58 44
Subtracted no value hepatocellular carcinoma-associated protein hca1. [refseq;acc:nm_020932] Measured 5430.7 23693.7 18263
melanoma-associated antigen 1 (mage-1 antigen) (antigen mz2-e). [swissprot;acc:p43355] Squared 89286 219048 129762
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 69 322 253
MYO5C myosin vc (myosin 5c). [swissprot;acc:q9nqx4] Rooted 20.106 146.94 167.046
27 Divided no value guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 like subunit. [swissprot;acc:q9y3k8] 1.66015 40.3364 24.2968
GNG4 guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-4 subunit. [swissprot;acc:p50150] Measured 2.04922 1834.33 895.134
NEUROD1 neurogenic differentiation factor 1 (neurod1) (neurod). [swissprot;acc:q13562] Squared 3.18404 143.692 457.521
SLC25A43 mitochondrial solute carrier protein. [refseq;acc:nm_145305] Ranked 1.31818 58 44
Subtracted no value myosin va (myosin 5a) (dilute myosin heavy chain, non-muscle) (myosin heavy chain 12) (myoxin). [swissprot;acc:q9y4i1] Rooted 20.106 146.94 167.046
GNAQ guanine nucleotide-binding protein g(q), alpha subunit. [swissprot;acc:p50148] Ranked 68.941 267.136 336.077
MAGEA10 melanoma-associated antigen 10 (mage-10 antigen). [swissprot;acc:p43363] Squared 89286 219048 129762
MAGEA6 melanoma-associated antigen 6 (mage-6 antigen) (mage3b). [swissprot;acc:p43360] Measured 5430.7 23693.7 18263
28 Divided ATF3 cyclic-amp-dependent transcription factor atf-3 (activating transcription factor 3). [swissprot;acc:p18847] Ranked 1.31416 201.949 153.671
GNG11 guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-11 subunit. [swissprot;acc:p50152] Rooted 1.65967 40.3372 24.3043
GNG3 guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-3 subunit. [swissprot;acc:p29798] Measured 2.04912 1834.36 895.194
NEUROD4 neurogenic differentiation factor 4 (neurod4). [swissprot;acc:q9hd90] Squared 3.18404 143.692 457.521
Subtracted GABARAP gaba(a) receptor-associated protein; gaba(a)-receptor-associated protein. [refseq;acc:nm_007278] Rooted 19.466 149.165 129.699
GNA11 guanine nucleotide-binding protein g(y), alpha subunit (alpha-11). [swissprot;acc:p29992] Ranked 68.941 267.136 336.077
MAGEB4 melanoma-associated antigen b1 (mage-b1 antigen) (mage-xp antigen) (dss-ahc critical interval mage superfamily 10) (dam10). [swissprot;acc:p43366] Squared 89286 219048 129762
NDN necdin. [swissprot;acc:q99608] Measured 5430.7 23693.7 18263
29 Divided CHD5 chromodomain helicase dna binding protein 5. [refseq;acc:nm_015557] Squared 3.18404 143.692 457.521
GNG8 guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-8 subunit (gamma-9). [swissprot;acc:q9uk08] Measured 2.04858 1834.52 895.507
PPP1R14A protein phosphatase 1, regulatory (inhibitor) subunit 14a; 17-kda pkc-potentiated inhibitory protein of pp1. [refseq;acc:nm_033256] Rooted 1.65937 26.0288 43.1914
PPP2R2D uncharacterized hematopoietic stem/progenitor cells protein mds026. [sptrembl;acc:q9nz48] Ranked 1.29991 187.458 243.678
Subtracted GNAZ guanine nucleotide-binding protein g(z), alpha subunit (g(x) alpha chain) (gz-alpha). [swissprot;acc:p19086] 68.936 267.139 336.075
MAGED1 melanoma-associated antigen d1 (mage-d1 antigen) (neurotrophin receptor-interacting mage homolog) (pro2292). [swissprot;acc:q9y5v3] Measured 5430.7 23693.7 18263
MAGED2 melanoma-associated antigen d2 (mage-d2 antigen) (breast cancer associated gene 1 protein) (bcg-1) (11b6) (hepatocellular carcinoma associated protein jcl-1). [swissprot;acc:q9unf1] Squared 89286 219048 129762

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/