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 182 to 231 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
Hugo
Value Type
description
Network Comparison Type
red
green
network_comparison
23 MRPS17 Ranked 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
CDK2AP2 Squared doc-1 related protein (doc-1r). [swissprot;acc:o75956] 143.692 457.521 3.18404
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] Subtracted 322 253 69
GNG5 Rooted guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 subunit. [swissprot;acc:p30670] Divided 40.3361 24.295 1.66026
MAGEA2B Measured melanoma-associated antigen 2 (mage-2 antigen). [swissprot;acc:p43356] Subtracted 23693.7 18263 5430.7
MAGEA4 Squared melanoma-associated antigen 12 (mage-12 antigen) (mage12f). [swissprot;acc:p43365] 219048 129762 89286
MYO5B Rooted myosin vb (myosin 5b) (fragment). [swissprot;acc:q9ulv0] 146.94 167.046 20.106
PANK2 Ranked pantothenate kinase 2, mitochondrial precursor (ec 2.7.1.33) (pantothenic acid kinase 2) (hpank2). [swissprot;acc:q9bz23] Divided 58 44 1.31818
26 no value Measured hepatocellular carcinoma-associated protein hca1. [refseq;acc:nm_020932] Subtracted 23693.7 18263 5430.7
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 69
Squared melanoma-associated antigen 1 (mage-1 antigen) (antigen mz2-e). [swissprot;acc:p43355] 219048 129762 89286
GNG10 Rooted guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-10 subunit. [swissprot;acc:p50151] Divided 40.3362 24.2954 1.66024
GNG12 Measured guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-12 subunit. [swissprot;acc:q9ubi6] 1833.01 892.67 2.0534
MYO5C Rooted myosin vc (myosin 5c). [swissprot;acc:q9nqx4] Subtracted 146.94 167.046 20.106
NEUROD6 Squared neurogenic differentiation factor 6 (neurod6) (my051 protein). [swissprot;acc:q96nk8] Divided 143.692 457.521 3.18404
PANK3 Ranked pantothenate kinase 3 (ec 2.7.1.33) (pantothenic acid kinase 3) (hpank3). [swissprot;acc:q9h999] 58 44 1.31818
27 no value Rooted guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 like subunit. [swissprot;acc:q9y3k8] 40.3364 24.2968 1.66015
myosin va (myosin 5a) (dilute myosin heavy chain, non-muscle) (myosin heavy chain 12) (myoxin). [swissprot;acc:q9y4i1] Subtracted 146.94 167.046 20.106
GNAQ Ranked guanine nucleotide-binding protein g(q), alpha subunit. [swissprot;acc:p50148] 267.136 336.077 68.941
GNG4 Measured guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-4 subunit. [swissprot;acc:p50150] Divided 1834.33 895.134 2.04922
MAGEA10 Squared melanoma-associated antigen 10 (mage-10 antigen). [swissprot;acc:p43363] Subtracted 219048 129762 89286
MAGEA6 Measured melanoma-associated antigen 6 (mage-6 antigen) (mage3b). [swissprot;acc:p43360] 23693.7 18263 5430.7
NEUROD1 Squared neurogenic differentiation factor 1 (neurod1) (neurod). [swissprot;acc:q13562] Divided 143.692 457.521 3.18404
SLC25A43 Ranked mitochondrial solute carrier protein. [refseq;acc:nm_145305] 58 44 1.31818
28 ATF3 cyclic-amp-dependent transcription factor atf-3 (activating transcription factor 3). [swissprot;acc:p18847] 201.949 153.671 1.31416
GABARAP Rooted gaba(a) receptor-associated protein; gaba(a)-receptor-associated protein. [refseq;acc:nm_007278] Subtracted 149.165 129.699 19.466
GNA11 Ranked guanine nucleotide-binding protein g(y), alpha subunit (alpha-11). [swissprot;acc:p29992] 267.136 336.077 68.941
GNG11 Rooted guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-11 subunit. [swissprot;acc:p50152] Divided 40.3372 24.3043 1.65967
GNG3 Measured guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-3 subunit. [swissprot;acc:p29798] 1834.36 895.194 2.04912
MAGEB4 Squared melanoma-associated antigen b1 (mage-b1 antigen) (mage-xp antigen) (dss-ahc critical interval mage superfamily 10) (dam10). [swissprot;acc:p43366] Subtracted 219048 129762 89286
NDN Measured necdin. [swissprot;acc:q99608] 23693.7 18263 5430.7
NEUROD4 Squared neurogenic differentiation factor 4 (neurod4). [swissprot;acc:q9hd90] Divided 143.692 457.521 3.18404
29 CHD5 chromodomain helicase dna binding protein 5. [refseq;acc:nm_015557]
GNAZ Ranked guanine nucleotide-binding protein g(z), alpha subunit (g(x) alpha chain) (gz-alpha). [swissprot;acc:p19086] Subtracted 267.139 336.075 68.936
GNG8 Measured guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-8 subunit (gamma-9). [swissprot;acc:q9uk08] Divided 1834.52 895.507 2.04858
MAGED1 melanoma-associated antigen d1 (mage-d1 antigen) (neurotrophin receptor-interacting mage homolog) (pro2292). [swissprot;acc:q9y5v3] Subtracted 23693.7 18263 5430.7
MAGED2 Squared 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] 219048 129762 89286
PPP1R14A Rooted protein phosphatase 1, regulatory (inhibitor) subunit 14a; 17-kda pkc-potentiated inhibitory protein of pp1. [refseq;acc:nm_033256] Divided 26.0288 43.1914 1.65937
PPP2R2D Ranked uncharacterized hematopoietic stem/progenitor cells protein mds026. [sptrembl;acc:q9nz48] 187.458 243.678 1.29991

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/