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 - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.


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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 394 to 443 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
green
network_comparison
99 mosaic protein lgn. [swissprot;acc:p81274] Rooted 47.6504 36.9304 1.29028
s-phase kinase-associated protein 1a (cyclin a/cdk2-associated protein p19) (p19a) (p19skp1) (rna polymerase ii elongation factor-like protein) (organ of corti protein 2) (ocp-ii protein) (ocp-2) (transcription elongation factor b) (siii). [swissprot;acc:p34991] Measured 2353.63 3225.65 1.3705
wd-repeat protein wdc146. [swissprot;acc:q9c0j8] Squared 226186 145568 1.55382
100 cleavage and polyadenylation specificity factor, 160 kda subunit (cpsf 160 kda subunit). [swissprot;acc:q10570]
f-box protein fbw7 isoform 2; archipelago, drosophila, homolog of; f-box protein fbw7; f-box protein sel-10; homolog of c elegans sel-10. [refseq;acc:nm_018315] Measured 2353.63 3225.65 1.3705
melanoma-associated antigen 10 (mage-10 antigen). [swissprot;acc:p43363] Ranked 88.2482 110.265 1.24949
regulator of g-protein signaling 17 (rgs17). [swissprot;acc:q9ugc6] Rooted 47.6504 36.9304 1.29028
101 cleavage and polyadenylation specificity factor, 100 kda subunit (cpsf 100 kda subunit) (fragment). [swissprot;acc:q9p2i0] Squared 222655 143584 1.5507
cullin homolog 2 (cul-2). [swissprot;acc:q13617] Measured 2353.63 3225.65 1.3705
guanine nucleotide-binding protein g(o), alpha subunit 1. [swissprot;acc:p09471] Rooted 47.6504 36.9304 1.29028
melanoma-associated antigen b1 (mage-b1 antigen) (mage-xp antigen) (dss-ahc critical interval mage superfamily 10) (dam10). [swissprot;acc:p43366] Ranked 88.2482 110.265 1.24949
102 fip1-like 1; rearranged in hypereosinophilia. [refseq;acc:nm_030917] Squared 214143 138337 1.54798
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] Ranked 88.2482 110.265 1.24949
presenilin 1 (ps-1) (s182 protein). [swissprot;acc:p49768] Measured 2353.63 3225.65 1.3705
rap1 gtpase-activating protein 1 (rap1gap). [swissprot;acc:p47736] Rooted 47.6504 36.9304 1.29028
103 cullin homolog 1 (cul-1). [swissprot;acc:q13616] Measured 2353.63 3225.65 1.3705
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 407289 263351 1.54656
proto-oncogene protein c-fos (cellular oncogene fos) (g0/g1 switch regulatory protein 7). [swissprot;acc:p01100] Rooted 60.8365 77.7233 1.27758
trophinin. [swissprot;acc:q12816] Ranked 88.2482 110.265 1.24949
104 cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438] Squared 407289 263351 1.54656
homer, neuronal immediate early gene, 2; homer homolog 3 (drosophila). [refseq;acc:nm_004839] Ranked 252.371 202.016 1.24926
jun dimerization protein. [refseq;acc:nm_130469] Rooted 60.8365 77.7233 1.27758
musashi 2 isoform a. [refseq;acc:nm_138962] Measured 4241.57 5810.79 1.36996
105 cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418] Squared 407289 263351 1.54656
fos-related antigen 2. [swissprot;acc:p15408] Rooted 60.8675 77.7168 1.27682
guanine nucleotide-binding protein g(i)/g(s)/g(t) beta subunit 1 (transducin beta chain 1). [swissprot;acc:p04901] Ranked 266.716 333.165 1.24914
musashi 1. [refseq;acc:nm_002442] Measured 4241.57 5810.79 1.36996
106 cytohesin 4. [swissprot;acc:q9uia0] Squared 407289 263351 1.54656
nuclear protein ukp68. [refseq;acc:nm_024824] Measured 4241.57 5810.79 1.36996
protein fosb (g0/g1 switch regulatory protein 3). [swissprot;acc:p53539] Rooted 60.8692 77.7165 1.27678
ubiquinone biosynthesis protein coq7 homolog (coenzyme q biosynthesis protein 7 homolog) (timing protein clk-1 homolog). [swissprot;acc:q99807] Ranked 252.329 202.004 1.24913
107 20 kda nuclear cap binding protein (ncbp 20 kda subunit) (cbp20) (ncbp interacting protein 1) (nip1). [swissprot;acc:p52298] Measured 4266.04 5843.51 1.36977
cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739] Squared 407289 263351 1.54656
fos-related antigen 1 (fra-1). [swissprot;acc:p15407] Rooted 60.875 77.7152 1.27664
homer, neuronal immediate early gene, 1b. [refseq;acc:nm_004272] Ranked 252.309 201.998 1.24907
108 filamin b, beta (actin binding protein 278); beta filamin; filamin 1 (actin-binding protein-280)-like; filamin b, beta (actin-binding protein-278); filamin b, beta. [refseq;acc:nm_001457] Measured 4366.44 5899.76 1.35116
homer, neuronal immediate early gene, 3. [refseq;acc:nm_004838] Ranked 252.296 201.995 1.24902
myosin heavy chain, cardiac muscle alpha isoform (myhc-alpha). [swissprot;acc:p13533] Squared 19321 12542.6 1.54043
voltage-dependent calcium channel gamma-2 subunit (neuronal voltage- gated calcium channel gamma-2 subunit). [swissprot;acc:q9y698] Rooted 49.2925 62.397 1.26585
109 guanine nucleotide-binding protein beta subunit 4 (transducin beta chain 4). [swissprot;acc:q9hav0] Ranked 266.933 333.281 1.24856
myosin heavy chain, skeletal muscle, fetal (myosin heavy chain iib) (myhc-iib). [swissprot;acc:q9y623] Squared 19321 12542.6 1.54043
rev1-like; rev1 protein; rev1 (yeast homolog)- like. [refseq;acc:nm_016316] Measured 4366.44 5899.76 1.35116
voltage-dependent calcium channel gamma-8 subunit (neuronal voltage- gated calcium channel gamma-8 subunit). [swissprot;acc:q8wxs5] Rooted 49.2923 62.3969 1.26585
110 deltex 2. [refseq;acc:nm_020892] Ranked 333.144 267.393 1.2459
myosin heavy chain, skeletal muscle, perinatal (myhc-perinatal). [swissprot;acc:p13535] Squared 19321 12542.6 1.54043
protein arginine n-methyltransferase 1 (ec 2.1.1.-) (interferon receptor 1-bound protein 4). [swissprot;acc:q99873] Measured 4366.44 5899.76 1.35116
voltage-dependent calcium channel gamma-4 subunit (neuronal voltage- gated calcium channel gamma-4 subunit). [swissprot;acc:q9ubn1] Rooted 49.293 62.3973 1.26585
111 deltex homolog 1; hdx-1. [refseq;acc:nm_004416] Ranked 332.925 267.274 1.24563
myosin heavy chain, skeletal muscle, adult 2 (myosin heavy chain iia) (myhc-iia). [swissprot;acc:q9ukx2] Squared 19321 12542.6 1.54043
protein arginine n-methyltransferase 4 (ec 2.1.1.-). [swissprot;acc:q9nr22] Measured 4366.44 5899.76 1.35116

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/