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 description Value Type Network Comparison Type Interaction Map red Filtered green network_comparison
Results: HTML CSV LaTeX Showing element 425 to 474 of 66312 in total
Filtered  : 1
Rank
description
Value Type
Network Comparison Type
Interaction Map
red
green
network_comparison
27 melanoma-associated antigen 10 (mage-10 antigen). [swissprot;acc:p43363] Squared Subtracted High confidence 219048 129762 89286
melanoma-associated antigen 6 (mage-6 antigen) (mage3b). [swissprot;acc:p43360] Measured 23693.7 18263 5430.7
microtubule-associated proteins 1a/1b light chain 3a (map1a/map1b lc3 a) (map1a/1b light chain 3 a). [swissprot;acc:q9h492] Squared Low confidence 78977.2 57161.1 21816.1
microtubule-associated proteins 1a/1b light chain 3b (map1a/map1b lc3 b) (map1a/1b light chain 3 b). [swissprot;acc:q9gzq8] Measured 13470.1 11654.4 1815.7
mitochondrial solute carrier protein. [refseq;acc:nm_145305] Ranked Divided High confidence 58 44 1.31818
myosin va (myosin 5a) (dilute myosin heavy chain, non-muscle) (myosin heavy chain 12) (myoxin). [swissprot;acc:q9y4i1] Rooted Subtracted 146.94 167.046 20.106
neurogenic differentiation factor 1 (neurod1) (neurod). [swissprot;acc:q13562] Squared Divided 143.692 457.521 3.18404
protein kinase, interferon-inducible double stranded rna dependent activator; protein activator of the interferon-induced protein kinase. [refseq;acc:nm_003690] Measured Low confidence 3840.85 4614.87 1.20152
28 atlastin; guanylate-binding protein 3. [refseq;acc:nm_015915] Ranked 142 170 1.19718
cyclic-amp-dependent transcription factor atf-3 (activating transcription factor 3). [swissprot;acc:p18847] High confidence 201.949 153.671 1.31416
Subtracted Low confidence 203.115 170.557 32.558
cytochrome p450 24a1, mitochondrial precursor (ec 1.14.-.-) (p450- cc24) (vitamin d(3) 24-hydroxylase) (1,25-dihydroxyvitamin d(3) 24- hydroxylase) (24-ohase). [swissprot;acc:q07973] Rooted 39.8493 52.9343 13.085
cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438] Squared 93450 72115.4 21334.6
gaba(a) receptor-associated protein; gaba(a)-receptor-associated protein. [refseq;acc:nm_007278] Rooted High confidence 149.165 129.699 19.466
glucosamine-6-phosphate isomerase (ec 3.5.99.6) (glucosamine-6- phosphate deaminase) (gnpda) (glcn6p deaminase) (oscillin). [swissprot;acc:p46926] Divided Low confidence 52.3425 45.0567 1.1617
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-11 subunit. [swissprot;acc:p50152] High confidence 40.3372 24.3043 1.65967
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-3 subunit. [swissprot;acc:p29798] Measured 1834.36 895.194 2.04912
guanine nucleotide-binding protein g(y), alpha subunit (alpha-11). [swissprot;acc:p29992] Ranked Subtracted 267.136 336.077 68.941
melanoma antigen, family d, 4 isoform 1; mage1 protein; mage-e1 protein; maged4 protein. [refseq;acc:nm_030801] Squared Divided Low confidence 82347.8 61881.5 1.33073
melanoma-associated antigen b1 (mage-b1 antigen) (mage-xp antigen) (dss-ahc critical interval mage superfamily 10) (dam10). [swissprot;acc:p43366] Subtracted High confidence 219048 129762 89286
microtubule-associated proteins 1a/1b light chain 3a (map1a/map1b lc3 a) (map1a/1b light chain 3 a). [swissprot;acc:q9h492] Measured Low confidence 13466.8 11652.4 1814.4
necdin. [swissprot;acc:q99608] High confidence 23693.7 18263 5430.7
neurogenic differentiation factor 4 (neurod4). [swissprot;acc:q9hd90] Squared Divided 143.692 457.521 3.18404
tob2 protein (transducer of erbb-2 2). [swissprot;acc:q14106] Measured Low confidence 3098.94 3719.66 1.2003
29 chromatin accessibility complex protein 1 (chrac-1) (chrac-15) (huchrac15) (dna polymerase epsilon subunit p15). [swissprot;acc:q9nrg0] Ranked Subtracted 250.244 217.843 32.401
chromodomain helicase dna binding protein 5. [refseq;acc:nm_015557] Squared Divided High confidence 143.692 457.521 3.18404
cyclic-amp-dependent transcription factor atf-3 (activating transcription factor 3). [swissprot;acc:p18847] Ranked Low confidence 203.115 170.557 1.19089
cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418] Squared Subtracted 92930.5 71802.4 21128.1
cytoplasmic polyadenylation element binding protein 3. [refseq;acc:nm_014912] Rooted Divided 48.8531 56.7071 1.16077
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-8 subunit (gamma-9). [swissprot;acc:q9uk08] Measured High confidence 1834.52 895.507 2.04858
guanine nucleotide-binding protein g(z), alpha subunit (g(x) alpha chain) (gz-alpha). [swissprot;acc:p19086] Ranked Subtracted 267.139 336.075 68.936
hepatocellular carcinoma-associated protein hca3. [refseq;acc:nm_138703] Squared Divided Low confidence 82347.8 61881.5 1.33073
melanoma-associated antigen d1 (mage-d1 antigen) (neurotrophin receptor-interacting mage homolog) (pro2292). [swissprot;acc:q9y5v3] Measured Subtracted High confidence 23693.7 18263 5430.7
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 219048 129762 89286
protein phosphatase 1, regulatory (inhibitor) subunit 14a; 17-kda pkc-potentiated inhibitory protein of pp1. [refseq;acc:nm_033256] Rooted Divided 26.0288 43.1914 1.65937
putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172] Subtracted 210.928 192.165 18.763
retinoblastoma-associated factor 600. [refseq;acc:nm_020765] Low confidence 76.5734 88.6244 12.051
septin 10 isoform 1. [refseq;acc:nm_144710] Measured 13081.2 14872.6 1791.4
tob1 protein (transducer of erbb-2 1). [swissprot;acc:p50616] Divided 3121.28 3739.84 1.19818
uncharacterized hematopoietic stem/progenitor cells protein mds026. [sptrembl;acc:q9nz48] Ranked High confidence 187.458 243.678 1.29991
30 bcl2-related ovarian killer. [refseq;acc:nm_032515] Low confidence 265.638 223.235 1.18995
bestrophin (vitelliform macular dystrophy protein) (tu15b). [swissprot;acc:o76090] Measured 36474.3 43509.4 1.19288
cyclic-amp-dependent transcription factor atf-3 (activating transcription factor 3). [swissprot;acc:p18847] Rooted Subtracted High confidence 60.8022 79.5099 18.7077
cyclin-dependent kinase 2-associated protein 1 (cdk2-associated protein 1) (putative oral cancer suppressor) (deleted in oral cancer- 1) (doc-1). [swissprot;acc:o14519] Squared Divided 143.692 457.521 3.18404
cytoplasmic polyadenylation element binding protein 4. [refseq;acc:nm_030627] Rooted Low confidence 48.8781 56.7253 1.16055
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 subunit. [swissprot;acc:p30670] Measured High confidence 1834.59 895.633 2.04837
guanine nucleotide-binding protein g(t), alpha-2 subunit (transducin alpha-2 chain). [swissprot;acc:p19087] Ranked Subtracted 267.14 336.075 68.935
mannosyl-oligosaccharide 1,2-alpha-mannosidase ib (ec 3.2.1.113) (processing alpha-1,2-mannosidase ib) (alpha-1,2-mannosidase ib) (mannosidase alpha class 1a member 2). [swissprot;acc:o60476] Squared Low confidence 92930 71802.1 21127.9
melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [swissprot;acc:p43357] Divided 82347.8 61881.5 1.33073
melanoma-associated antigen f1 (mage-f1 antigen). [swissprot;acc:q9hay2] Measured Subtracted High confidence 23693.7 18263 5430.7

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
- 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/