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 Value Type Hugo description Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 873 to 922 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
Value Type
Hugo
description
red
green
network_comparison
219 Measured no value transforming protein n-ras. [swissprot;acc:p01111] 16069.8 12885.6 1.24711
Ranked MYH3 myosin heavy chain, fast skeletal muscle, embryonic (muscle embryonic myosin heavy chain) (smhce). [swissprot;acc:p11055] 112 126 1.125
Squared COX4I1 cytochrome c oxidase subunit iv isoform 1, mitochondrial precursor (ec 1.9.3.1) (cox iv-1) (cytochrome c oxidase polypeptide iv). [swissprot;acc:p13073] 86600.9 65229.9 1.32763
Rooted RBBP7 histone acetyltransferase type b subunit 2 (retinoblastoma binding protein p46) (retinoblastoma-binding protein 7) (rbbp-7). [swissprot;acc:q16576] 52.7146 60.0088 1.13837
220 Measured no value 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] 41482.5 33356.5 1.24361
Ranked MYH1 myosin heavy chain, skeletal muscle, adult 1 (myosin heavy chain iix/d) (myhc-iix/d). [swissprot;acc:p12882] 112 126 1.125
Squared COX4I2 cytochrome c oxidase subunit iv isoform 2, mitochondrial precursor (ec 1.9.3.1) (cox iv-2). [swissprot;acc:q96kj9] 86600.9 65229.9 1.32763
Rooted MTA1 metastasis-associated protein mta1. [swissprot;acc:q13330] 52.7557 60.035 1.13798
221 Measured PSCD1 cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438] 41482.5 33356.5 1.24361
Ranked no value myosin heavy chain, cardiac muscle beta isoform (myhc-beta). [swissprot;acc:p12883] 112 126 1.125
Squared HPRT1 hypoxanthine-guanine phosphoribosyltransferase (ec 2.4.2.8) (hgprt) (hgprtase). [swissprot;acc:p00492] 70739 93908.8 1.32754
Rooted TXNL4A spliceosomal u5 snrnp-specific 15 kda protein (dim1 protein homolog) (thioredoxin-like u5 snrnp protein u5-15kd). [swissprot;acc:o14834] 56.9506 64.7888 1.13763
222 Measured PSCD2 cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418] 41482.5 33356.5 1.24361
Ranked MYH7B dj756n5.1.1 (continues in em:al133324 as dj1161h23.3) (fragment). [sptrembl;acc:q9h430] 112 126 1.125
Squared STAM2 signal transducing adaptor molecule 2; stam-like protein containing sh3 and itam domains 2. [refseq;acc:nm_005843] 86281 65058.3 1.32621
Rooted RBBP4 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] 52.7936 60.0592 1.13762
223 Measured PSCD4 cytohesin 4. [swissprot;acc:q9uia0] 41482.5 33356.5 1.24361
Ranked MYH13 myosin heavy chain, skeletal muscle, extraocular (myhc-eo). [swissprot;acc:q9ukx3] 112 126 1.125
Squared TCP1 t-complex protein 1, alpha subunit (tcp-1-alpha) (cct-alpha). [swissprot;acc:p17987] 40982.6 54272.3 1.32428
Rooted MAGED4 melanoma antigen, family d, 4 isoform 1; mage1 protein; mage-e1 protein; maged4 protein. [refseq;acc:nm_030801] 137.446 120.823 1.13758
224 Measured PSCD3 cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739] 41482.5 33356.5 1.24361
Ranked SLC15A2 oligopeptide transporter, kidney isoform (peptide transporter 2) (kidney h+/peptide cotransporter) (solute carrier family 15, member 2). [swissprot;acc:q16348] 185.969 165.623 1.12285
Squared SNRPD1 small nuclear ribonucleoprotein sm d1 (snrnp core protein d1) (sm-d1) (sm-d autoantigen). [swissprot;acc:p13641] 14943.9 19771.9 1.32307
Rooted MAGEE2 hepatocellular carcinoma-associated protein hca3. [refseq;acc:nm_138703] 137.446 120.823 1.13758
225 Measured no value myosin heavy chain, cardiac muscle alpha isoform (myhc-alpha). [swissprot;acc:p13533] 9035 7279.6 1.24114
Ranked SNRPD2 small nuclear ribonucleoprotein sm d2 (snrnp core protein d2) (sm-d2). [swissprot;acc:p43330] 226.471 201.769 1.12243
Squared MTX1 metaxin 1. [swissprot;acc:q13505] 60401.6 79875.7 1.32241
Rooted no value melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [swissprot;acc:p43357] 137.446 120.823 1.13758
226 Measured MYH4 myosin heavy chain, skeletal muscle, fetal (myosin heavy chain iib) (myhc-iib). [swissprot;acc:q9y623] 9035 7279.6 1.24114
Ranked COMP cartilage oligomeric matrix protein precursor (comp). [swissprot;acc:p49747] 239.991 269.238 1.12187
Squared SLC15A2 oligopeptide transporter, kidney isoform (peptide transporter 2) (kidney h+/peptide cotransporter) (solute carrier family 15, member 2). [swissprot;acc:q16348] 73510.2 55607.3 1.32195
Rooted MAGEA11 melanoma-associated antigen 11 (mage-11 antigen). [swissprot;acc:p43364] 137.446 120.823 1.13758
227 Measured MYH8 myosin heavy chain, skeletal muscle, perinatal (myhc-perinatal). [swissprot;acc:p13535] 9035 7279.6 1.24114
Ranked THBS3 thrombospondin 3 precursor. [swissprot;acc:p49746] 239.99 269.234 1.12186
Squared SLC15A1 oligopeptide transporter, small intestine isoform (peptide transporter 1) (intestinal h+/peptide cotransporter) (solute carrier family 15, member 1). [swissprot;acc:p46059] 73995.1 56003.7 1.32125
Rooted MAGEA2B melanoma-associated antigen 2 (mage-2 antigen). [swissprot;acc:p43356] 137.446 120.823 1.13758
228 Measured MYH2 myosin heavy chain, skeletal muscle, adult 2 (myosin heavy chain iia) (myhc-iia). [swissprot;acc:q9ukx2] 9035 7279.6 1.24114
Ranked SH2D3C sh2 domain containing 3c; novel sh2-containing protein 3; sh2 domain-containing 3c; likely ortholog of mouse cas/hef1-associated signal transducer. [refseq;acc:nm_005489] 226.411 202.088 1.12036
Squared ECHS1 enoyl-coa hydratase, mitochondrial precursor (ec 4.2.1.17) (short chain enoyl-coa hydratase) (sceh) (enoyl-coa hydratase 1). [swissprot;acc:p30084] 57913.5 76336.3 1.31811
Rooted no value hepatocellular carcinoma-associated protein hca1. [refseq;acc:nm_020932] 137.446 120.823 1.13758
229 Measured MYH3 myosin heavy chain, fast skeletal muscle, embryonic (muscle embryonic myosin heavy chain) (smhce). [swissprot;acc:p11055] 9035 7279.6 1.24114
Ranked BCAR3 breast cancer antiestrogen resistance 3. [refseq;acc:nm_003567] 226.401 202.094 1.12028
Squared MAPK11 mitogen-activated protein kinase 12 (ec 2.7.1.37) (extracellular signal-regulated kinase 6) (erk-6) (erk5) (stress-activated protein kinase-3) (mitogen-activated protein kinase p38 gamma) (map kinase p38 gamma). [swissprot;acc:p53778] 42411.6 55802.1 1.31573
Rooted MAGEA6 melanoma-associated antigen 6 (mage-6 antigen) (mage3b). [swissprot;acc:p43360] 137.446 120.823 1.13758
230 Measured MYH1 myosin heavy chain, skeletal muscle, adult 1 (myosin heavy chain iix/d) (myhc-iix/d). [swissprot;acc:p12882] 9035 7279.6 1.24114
Ranked CSRP1 cysteine-rich protein 1 (crp1) (crp). [swissprot;acc:p21291] 239.35 267.915 1.11934
Squared SPHK1 sphingosine kinase 1 (ec 2.7.1.-) (sk 1) (spk 1). [swissprot;acc:q9nya1] 42411.6 55802.1 1.31573
Rooted NDN necdin. [swissprot;acc:q99608] 137.446 120.823 1.13758
231 Measured no value myosin heavy chain, cardiac muscle beta isoform (myhc-beta). [swissprot;acc:p12883] 9035 7279.6 1.24114
Ranked SHCBP1 likely ortholog of mouse shc sh2-domain binding protein 1. [refseq;acc:nm_024745] 239.336 267.881 1.11927

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/