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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Gene Rank description Network Comparison Type Value Type Interaction Map green Filtered network_comparison red
Results: HTML CSV LaTeX Showing element 29792 to 29841 of 66312 in total
Filtered  : 1
Rank
description
Network Comparison Type
Value Type
Interaction Map
green
network_comparison
red
1862 ww domain binding protein 2 (wbp-2). [swissprot;acc:q969t9] Divided Squared Low confidence 43627.8 1.04118 45424.4
1863 15-hydroxyprostaglandin dehydrogenase [nad(+)] (ec 1.1.1.141) (pgdh). [swissprot;acc:p15428] Subtracted Measured 8425.81 260.01 8165.8
60s acidic ribosomal protein p2. [swissprot;acc:p05387] Ranked 200.886 3.922 204.808
adhesion regulating molecule 1 precursor (110 kda cell membrane glycoprotein) (gp110). [swissprot;acc:q16186] Measured High confidence 6195.48 369.48 5826
aminoadipate-semialdehyde synthase; lysine-ketoglutarate reductase /saccharopine dehydrogenase; lysine-2-oxoglutarate reductase; aminoadipic semialdehyde synthase. [refseq;acc:nm_005763] Divided Low confidence 8345.43 1.03267 8081.38
autophagy protein 5-like (apg5-like) (apoptosis-specific protein). [swissprot;acc:q9h1y0] Subtracted Rooted 73.74 2.5532 71.1868
fragile x mental retardation 1 protein (protein fmr-1) (fmrp). [swissprot;acc:q06787] Ranked High confidence 200.115 2.295 202.41
g-rich sequence factor-1 (grsf-1). [swissprot;acc:q12849] Divided Squared 29336.9 1.09552 26779
glycogenin-1 (ec 2.4.1.186). [swissprot;acc:p46976] Subtracted Rooted 67.8076 1.8784 65.9292
histone h3.1 (h3/a) (h3/c) (h3/d) (h3/f) (h3/h) (h3/i) (h3/j) (h3/k) (h3/l). [swissprot;acc:p16106] Divided Squared Low confidence 43985.3 1.04117 45796
keratin, ultra high-sulfur matrix protein b (uhs keratin b) (uhs kerb). [swissprot;acc:o75690] Measured High confidence 6463.14 1.0636 6076.66
nadh-cytochrome b5 reductase (ec 1.6.2.2) (b5r). [swissprot;acc:p00387] Ranked 213.147 1.01087 210.856
nefa-interacting nuclear protein nip30. [refseq;acc:nm_024946] Rooted 65.1018 1.0296 63.2302
protein kinase c substrate, 80 kda protein, heavy chain (pkcsh) (80k-h protein). [swissprot;acc:p14314] Low confidence 73.8645 1.0354 71.3392
ring finger protein 111; arkadia. [refseq;acc:nm_017610] Subtracted Squared 43161.5 1802.1 44963.6
seven in absentia homolog 1. [refseq;acc:nm_003031] High confidence 26329.1 2208 24121.1
uv excision repair protein rad23 homolog b (hhr23b) (xp-c repair complementing complex 58 kda protein) (p58). [swissprot;acc:p54727] Divided Ranked Low confidence 199.474 1.01988 203.439
1864 adenosine kinase (ec 2.7.1.20) (ak) (adenosine 5'-phosphotransferase). [swissprot;acc:p55263] Subtracted Rooted High confidence 67.8076 1.8784 65.9292
camp response element-binding protein cre-bpa. [refseq;acc:nm_004904] Squared 27002 2205.7 24796.3
cyclin-dependent kinases regulatory subunit 2 (cks-2). [swissprot;acc:p33552] Divided Rooted Low confidence 74.4429 1.0354 71.8978
fasciculation and elongation protein zeta 1 (zygin i). [swissprot;acc:q99689] Measured 8240.15 1.03266 7979.57
fuse-binding protein-interacting repressor isoform b; siah binding protein 1; pyrimidine tract binding splicing factor; ro ribonucleoprotein-binding protein 1; poly-u binding splicing factor puf60. [refseq;acc:nm_014281] Ranked High confidence 200.89 1.01086 203.071
heterogeneous nuclear ribonucleoprotein h3 (hnrnp h3) (hnrnp 2h9). [swissprot;acc:p31942] Squared 29336.2 1.09552 26778.4
importin beta-3 subunit (karyopherin beta-3 subunit) (ran-binding protein 5). [swissprot;acc:o00410] Ranked Low confidence 197.236 1.01988 201.157
keratin, ultra high-sulfur matrix protein a (uhs keratin a) (uhs kera). [swissprot;acc:p26371] Measured High confidence 6463.14 1.0636 6076.66
lim homeobox transcription factor 1 alpha (lim/homeobox protein lmx1a) (lim-homeobox protein 1.1) (lmx-1.1). [swissprot;acc:q8te12] Rooted 65.1018 1.0296 63.2302
ornithine aminotransferase, mitochondrial precursor (ec 2.6.1.13) (ornithine--oxo-acid aminotransferase). [swissprot;acc:p04181] Subtracted Squared Low confidence 46760.2 1801.9 48562.1
peptide deformylase, mitochondrial precursor (ec 3.5.1.88) (pdf) (polypeptide deformylase). [swissprot;acc:q9hbh1] Measured 8425.81 260.01 8165.8
poly(a) binding protein, nuclear 1; oculopharyngeal muscular dystrophy; poly(a)-binding protein, nuclear 1; poly(a) binding protein ii; poly(a) binding protein 2. [refseq;acc:nm_004643] Divided Squared 42371.7 1.04117 44116.1
probable glutamyl-trna(gln) amidotransferase subunit b, mitochondrial precursor (ec 6.3.5.-) (glu-adt subunit b) (cytochrome oxidase assembly factor pet112 homolog). [swissprot;acc:o75879] Subtracted Ranked 196.475 3.922 200.397
protocadherin 15 precursor. [swissprot;acc:q96qu1] Rooted 74.7307 2.5526 72.1781
putative gtp-binding protein ptd004 (pro2455). [swissprot;acc:q9ntk5] Ranked High confidence 217.373 2.292 215.081
ubiquitin carboxyl-terminal hydrolase isozyme l5 (ec 3.4.19.12) (uch- l5) (ubiquitin thiolesterase l5) (ubiquitin c-terminal hydrolase uch37) (cgi-70) (ad-019). [swissprot;acc:q9y5k5] Measured 6195.48 369.48 5826
1865 acyl-coa dehydrogenase, medium-chain specific, mitochondrial precursor (ec 1.3.99.3) (mcad). [swissprot;acc:p11310] Divided Low confidence 8206.59 1.03266 7947.06
chromodomain-helicase-dna-binding protein 2 (chd-2). [swissprot;acc:o14647] Subtracted Ranked 198.255 3.921 202.176
cytochrome b5 reductase b5r.2. [refseq;acc:nm_016229] High confidence 213.147 2.291 210.856
delta 1-pyrroline-5-carboxylate synthetase (p5cs) [includes: glutamate 5-kinase (ec 2.7.2.11) (gamma-glutamyl kinase) (gk); gamma-glutamyl phosphate reductase (gpr) (ec 1.2.1.41) (glutamate-5-semialdehyde dehydrogenase) (glutamyl-gamma-semialdehyde dehydrogenase)]. [swissprot;acc:p54886] Rooted Low confidence 75.1324 2.5526 72.5798
eukaryotic translation initiation factor 2 subunit 3 (eukaryotic translation initiation factor 2 gamma subunit) (eif-2-gamma). [swissprot;acc:p41091] Divided Ranked High confidence 224.046 1.01086 221.639
glycerol kinase, testis specific 2 (ec 2.7.1.30) (atp:glycerol 3- phosphotransferase) (glycerokinase) (gk). [swissprot;acc:q14410] Low confidence 196.809 1.01987 200.72
heterogeneous nuclear ribonucleoprotein f (hnrnp f). [swissprot;acc:p52597] Squared High confidence 29334.8 1.09551 26777.3
metastasis-associated protein mta1. [swissprot;acc:q13330] Subtracted Measured Low confidence 7957.79 259.99 7697.8
mitochondrial precursor proteins import receptor (translocase of outer membrane tom70). [swissprot;acc:o94826] Divided Rooted High confidence 65.1018 1.0296 63.2302
presynaptic protein sap97 (synapse-associated protein 97) (discs, large homolog 1) (hdlg). [swissprot;acc:q12959] Subtracted Squared 28784.7 2200.7 26584
protein x 0001. [refseq;acc:nm_016302] Rooted 67.8076 1.8784 65.9292
rna polymerase ii subunit 5-mediating protein (rpb5-mediating protein). [swissprot;acc:o94763] Measured 6195.48 369.48 5826
rna-binding region containing protein 1 (hsrnaseb) (ssdna binding protein seb4) (cll-associated antigen kw-5). [swissprot;acc:q9h0z9] Squared Low confidence 43160.3 1801.5 44961.8
star-related lipid transfer protein 5 (stard5) (start domain- containing protein 5). [swissprot;acc:q9nsy2] Divided Measured High confidence 6463.12 1.0636 6076.66
transgelin (smooth muscle protein 22-alpha) (sm22-alpha) (ws3-10) (22 kda actin-binding protein). [swissprot;acc:q01995] Squared Low confidence 37566.4 1.04115 39112.4
udp-galactose translocator (udp-galactose transporter) (ugt) (udp-gal- tr). [swissprot;acc:p78381] Rooted 73.8546 1.0354 71.3297
1866 brefeldin a-inhibited guanine nucleotide-exchange protein 2 (brefeldin a-inhibited gep 2). [swissprot;acc:q9y6d5] Subtracted Measured 8278.28 259.88 8018.4

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/