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 Value Type Gene description Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 401 to 450 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
Value Type
description
red
green
network_comparison
101 Measured cullin homolog 2 (cul-2). [swissprot;acc:q13617] 2353.63 3225.65 1.3705
Ranked melanoma-associated antigen b1 (mage-b1 antigen) (mage-xp antigen) (dss-ahc critical interval mage superfamily 10) (dam10). [swissprot;acc:p43366] 88.2482 110.265 1.24949
Squared cleavage and polyadenylation specificity factor, 100 kda subunit (cpsf 100 kda subunit) (fragment). [swissprot;acc:q9p2i0] 222655 143584 1.5507
Rooted guanine nucleotide-binding protein g(o), alpha subunit 1. [swissprot;acc:p09471] 47.6504 36.9304 1.29028
102 Measured presenilin 1 (ps-1) (s182 protein). [swissprot;acc:p49768] 2353.63 3225.65 1.3705
Ranked 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] 88.2482 110.265 1.24949
Squared fip1-like 1; rearranged in hypereosinophilia. [refseq;acc:nm_030917] 214143 138337 1.54798
Rooted rap1 gtpase-activating protein 1 (rap1gap). [swissprot;acc:p47736] 47.6504 36.9304 1.29028
103 Measured cullin homolog 1 (cul-1). [swissprot;acc:q13616] 2353.63 3225.65 1.3705
Ranked trophinin. [swissprot;acc:q12816] 88.2482 110.265 1.24949
Squared 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] 407289 263351 1.54656
Rooted proto-oncogene protein c-fos (cellular oncogene fos) (g0/g1 switch regulatory protein 7). [swissprot;acc:p01100] 60.8365 77.7233 1.27758
104 Measured musashi 2 isoform a. [refseq;acc:nm_138962] 4241.57 5810.79 1.36996
Ranked homer, neuronal immediate early gene, 2; homer homolog 3 (drosophila). [refseq;acc:nm_004839] 252.371 202.016 1.24926
Squared cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438] 407289 263351 1.54656
Rooted jun dimerization protein. [refseq;acc:nm_130469] 60.8365 77.7233 1.27758
105 Measured musashi 1. [refseq;acc:nm_002442] 4241.57 5810.79 1.36996
Ranked guanine nucleotide-binding protein g(i)/g(s)/g(t) beta subunit 1 (transducin beta chain 1). [swissprot;acc:p04901] 266.716 333.165 1.24914
Squared cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418] 407289 263351 1.54656
Rooted fos-related antigen 2. [swissprot;acc:p15408] 60.8675 77.7168 1.27682
106 Measured nuclear protein ukp68. [refseq;acc:nm_024824] 4241.57 5810.79 1.36996
Ranked ubiquinone biosynthesis protein coq7 homolog (coenzyme q biosynthesis protein 7 homolog) (timing protein clk-1 homolog). [swissprot;acc:q99807] 252.329 202.004 1.24913
Squared cytohesin 4. [swissprot;acc:q9uia0] 407289 263351 1.54656
Rooted protein fosb (g0/g1 switch regulatory protein 3). [swissprot;acc:p53539] 60.8692 77.7165 1.27678
107 Measured 20 kda nuclear cap binding protein (ncbp 20 kda subunit) (cbp20) (ncbp interacting protein 1) (nip1). [swissprot;acc:p52298] 4266.04 5843.51 1.36977
Ranked homer, neuronal immediate early gene, 1b. [refseq;acc:nm_004272] 252.309 201.998 1.24907
Squared cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739] 407289 263351 1.54656
Rooted fos-related antigen 1 (fra-1). [swissprot;acc:p15407] 60.875 77.7152 1.27664
108 Measured 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] 4366.44 5899.76 1.35116
Ranked homer, neuronal immediate early gene, 3. [refseq;acc:nm_004838] 252.296 201.995 1.24902
Squared myosin heavy chain, cardiac muscle alpha isoform (myhc-alpha). [swissprot;acc:p13533] 19321 12542.6 1.54043
Rooted voltage-dependent calcium channel gamma-2 subunit (neuronal voltage- gated calcium channel gamma-2 subunit). [swissprot;acc:q9y698] 49.2925 62.397 1.26585
109 Measured rev1-like; rev1 protein; rev1 (yeast homolog)- like. [refseq;acc:nm_016316] 4366.44 5899.76 1.35116
Ranked guanine nucleotide-binding protein beta subunit 4 (transducin beta chain 4). [swissprot;acc:q9hav0] 266.933 333.281 1.24856
Squared myosin heavy chain, skeletal muscle, fetal (myosin heavy chain iib) (myhc-iib). [swissprot;acc:q9y623] 19321 12542.6 1.54043
Rooted voltage-dependent calcium channel gamma-8 subunit (neuronal voltage- gated calcium channel gamma-8 subunit). [swissprot;acc:q8wxs5] 49.2923 62.3969 1.26585
110 Measured protein arginine n-methyltransferase 1 (ec 2.1.1.-) (interferon receptor 1-bound protein 4). [swissprot;acc:q99873] 4366.44 5899.76 1.35116
Ranked deltex 2. [refseq;acc:nm_020892] 333.144 267.393 1.2459
Squared myosin heavy chain, skeletal muscle, perinatal (myhc-perinatal). [swissprot;acc:p13535] 19321 12542.6 1.54043
Rooted voltage-dependent calcium channel gamma-4 subunit (neuronal voltage- gated calcium channel gamma-4 subunit). [swissprot;acc:q9ubn1] 49.293 62.3973 1.26585
111 Measured protein arginine n-methyltransferase 4 (ec 2.1.1.-). [swissprot;acc:q9nr22] 4366.44 5899.76 1.35116
Ranked deltex homolog 1; hdx-1. [refseq;acc:nm_004416] 332.925 267.274 1.24563
Squared myosin heavy chain, skeletal muscle, adult 2 (myosin heavy chain iia) (myhc-iia). [swissprot;acc:q9ukx2] 19321 12542.6 1.54043
Rooted voltage-dependent calcium channel gamma-3 subunit (neuronal voltage- gated calcium channel gamma-3 subunit). [swissprot;acc:o60359] 49.2923 62.3969 1.26585
112 Measured u1 small nuclear ribonucleoprotein 70 kda (u1 snrnp 70 kda) (snrnp70) (u1-70k). [swissprot;acc:p08621] 4366.44 5899.76 1.35116
Ranked t-lak cell-originated protein kinase; spermatogenesis-related protein kinase; pdz-binding kinase; pbk; mapkk-like protein kinase; serine/threonine protein kinase. [refseq;acc:nm_018492] 332.874 267.246 1.24557
Squared myosin heavy chain, fast skeletal muscle, embryonic (muscle embryonic myosin heavy chain) (smhce). [swissprot;acc:p11055] 19321 12542.6 1.54043
Rooted voltage-dependent calcium channel gamma-5 subunit (neuronal voltage- gated calcium channel gamma-5 subunit). [swissprot;acc:q9uf02] 49.3267 62.4167 1.26537
113 Measured filamin a (alpha-filamin) (filamin 1) (endothelial actin-binding protein) (abp-280) (nonmuscle filamin). [swissprot;acc:p21333] 4366.44 5899.76 1.35116
Ranked kh domain containing, rna binding, signal transduction associated 3; sam68-like phosphotyrosine protein, t-star. [refseq;acc:nm_006558] 332.874 267.246 1.24557

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/