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 Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 1750 to 1799 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
Network Comparison Type
red
green
network_comparison
219 myosin heavy chain, fast skeletal muscle, embryonic (muscle embryonic myosin heavy chain) (smhce). [swissprot;acc:p11055] Ranked Divided 112 126 1.125
transforming protein n-ras. [swissprot;acc:p01111] Measured 16069.8 12885.6 1.24711
tyrosine-protein kinase hck (ec 2.7.1.112) (p59-hck/p60-hck) (hemopoietic cell kinase). [swissprot;acc:p08631] Subtracted 6417.18 7859.6 1442.42
220 brain protein 44. [swissprot;acc:o95563] Rooted 113.374 123.463 10.089
crk-like protein. [swissprot;acc:p46109] Measured 6417.18 7859.6 1442.42
cytochrome c oxidase subunit iv isoform 2, mitochondrial precursor (ec 1.9.3.1) (cox iv-2). [swissprot;acc:q96kj9] Squared Divided 86600.9 65229.9 1.32763
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] Measured 41482.5 33356.5 1.24361
metastasis-associated protein mta1. [swissprot;acc:q13330] Rooted 52.7557 60.035 1.13798
mitochondrial ribosomal protein l2. [refseq;acc:nm_015950] Ranked Subtracted 242.339 266.986 24.647
myosin heavy chain, skeletal muscle, adult 1 (myosin heavy chain iix/d) (myhc-iix/d). [swissprot;acc:p12882] Divided 112 126 1.125
transcription initiation factor tfiid 55 kda subunit (tafii-55) (tafii55). [swissprot;acc:q15545] Squared Subtracted 57808.9 46630.3 11178.6
221 cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438] Measured Divided 41482.5 33356.5 1.24361
hypoxanthine-guanine phosphoribosyltransferase (ec 2.4.2.8) (hgprt) (hgprtase). [swissprot;acc:p00492] Squared 70739 93908.8 1.32754
myosin heavy chain, cardiac muscle beta isoform (myhc-beta). [swissprot;acc:p12883] Ranked 112 126 1.125
protein translation factor sui1 homolog gc20. [swissprot;acc:o60739] Subtracted 242.627 267.151 24.524
proto-oncogene tyrosine-protein kinase fyn (ec 2.7.1.112) (p59-fyn) (syn) (slk). [swissprot;acc:p06241] Measured 6417.18 7859.6 1442.42
septin 7 (cdc10 protein homolog). [swissprot;acc:q16181] Rooted 113.374 123.463 10.089
spliceosomal u5 snrnp-specific 15 kda protein (dim1 protein homolog) (thioredoxin-like u5 snrnp protein u5-15kd). [swissprot;acc:o14834] Divided 56.9506 64.7888 1.13763
tata box binding protein-associated factor, rna polymerase ii, q; taf7-like rna polymerase ii, tata box binding protein (tbp)-associated factor, 50 kd; tbp-associated factor, rna polymerase ii, q. [refseq;acc:nm_024885] Squared Subtracted 57579.2 46497.2 11082
222 60s ribosomal protein l14 (cag-isl 7). [swissprot;acc:p50914] Ranked 242.153 266.673 24.52
chromatin assembly factor 1 subunit c (caf-1 subunit c) (chromatin assembly factor i p48 subunit) (caf-i 48 kda subunit) (caf-ip48) (retinoblastoma binding protein p48) (retinoblastoma-binding protein 4) (rbbp-4) (msi1 protein homolog). [swissprot;acc:q09028] Rooted Divided 52.7936 60.0592 1.13762
cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418] Measured 41482.5 33356.5 1.24361
dj756n5.1.1 (continues in em:al133324 as dj1161h23.3) (fragment). [sptrembl;acc:q9h430] Ranked 112 126 1.125
lag1 longevity assurance homolog 2 isoform 1; l3 pigment; tumor metastasis-suppressor. [refseq;acc:nm_022075] Rooted Subtracted 61.6639 71.7355 10.0716
metalloprotease 1; metalloprotease 1 (pitrilysin family). [refseq;acc:nm_014889] Squared 29570.7 18601.8 10968.9
proto-oncogene tyrosine-protein kinase fgr (ec 2.7.1.112) (p55-fgr) (c-fgr). [swissprot;acc:p09769] Measured 6417.18 7859.6 1442.42
signal transducing adaptor molecule 2; stam-like protein containing sh3 and itam domains 2. [refseq;acc:nm_005843] Squared Divided 86281 65058.3 1.32621
223 beta-1,4 mannosyltransferase. [refseq;acc:nm_019109] Subtracted 29567 18601.6 10965.4
cytohesin 4. [swissprot;acc:q9uia0] Measured Divided 41482.5 33356.5 1.24361
melanoma antigen, family d, 4 isoform 1; mage1 protein; mage-e1 protein; maged4 protein. [refseq;acc:nm_030801] Rooted 137.446 120.823 1.13758
myosin heavy chain, skeletal muscle, extraocular (myhc-eo). [swissprot;acc:q9ukx3] Ranked 112 126 1.125
septin 6. [swissprot;acc:q14141] Rooted Subtracted 113.169 123.23 10.061
serine racemase (ec 5.1.1.-). [swissprot;acc:q9gzt4] Ranked 242.153 266.673 24.52
t-complex protein 1, alpha subunit (tcp-1-alpha) (cct-alpha). [swissprot;acc:p17987] Squared Divided 40982.6 54272.3 1.32428
tyrosine-protein kinase abl2 (ec 2.7.1.112) (tyrosine kinase arg). [swissprot;acc:p42684] Measured Subtracted 6417.18 7859.59 1442.41
224 60s ribosomal protein l34. [swissprot;acc:p49207] Ranked 242.153 266.673 24.52
cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739] Measured Divided 41482.5 33356.5 1.24361
dna polymerase epsilon p12 subunit (dna polymerase epsilon subunit 4). [swissprot;acc:q9nr33] Rooted Subtracted 44.849 54.7964 9.9474
galectin-4 (lactose-binding lectin 4) (l-36 lactose binding protein) (l36lbp) (antigen ny-co-27). [swissprot;acc:p56470] Squared 46021.4 56813.2 10791.8
hepatocellular carcinoma-associated protein hca3. [refseq;acc:nm_138703] Rooted Divided 137.446 120.823 1.13758
oligopeptide transporter, kidney isoform (peptide transporter 2) (kidney h+/peptide cotransporter) (solute carrier family 15, member 2). [swissprot;acc:q16348] Ranked 185.969 165.623 1.12285
proto-oncogene tyrosine-protein kinase abl1 (ec 2.7.1.112) (p150) (c-abl). [swissprot;acc:p00519] Measured Subtracted 6417.18 7859.59 1442.41
small nuclear ribonucleoprotein sm d1 (snrnp core protein d1) (sm-d1) (sm-d autoantigen). [swissprot;acc:p13641] Squared Divided 14943.9 19771.9 1.32307
225 grb2-related adaptor protein 2 (gads protein) (growth factor receptor binding protein) (grblg) (grf40 adaptor protein) (grf-40) (grb-2-like protein) (grb2l) (grbx) (p38) (hematopoietic cell-associated adaptor protein grpl) (adapter protein grid) (sh3-sh2-sh3 adaptor mona). [swissprot;acc:o75791] Measured Subtracted 6417.19 7859.51 1442.32
melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [swissprot;acc:p43357] Rooted Divided 137.446 120.823 1.13758
metaxin 1. [swissprot;acc:q13505] Squared 60401.6 79875.7 1.32241
myosin heavy chain, cardiac muscle alpha isoform (myhc-alpha). [swissprot;acc:p13533] Measured 9035 7279.6 1.24114
protein 4.1 (band 4.1) (p4.1) (epb4.1) (4.1r). [swissprot;acc:p11171] Squared Subtracted 45986 56776.1 10790.1
protein transport protein sec61 alpha subunit isoform 2 (sec61 alpha- 2). [swissprot;acc:q9y2r3] Ranked 242.153 266.673 24.52
small nuclear ribonucleoprotein sm d2 (snrnp core protein d2) (sm-d2). [swissprot;acc:p43330] Divided 226.471 201.769 1.12243

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/