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 4808 to 4857 of 66312 in total
Filtered  : 1
Rank
description
Value Type
Network Comparison Type
Interaction Map
red
green
network_comparison
301 integrin alpha-5 precursor (fibronectin receptor alpha subunit) (integrin alpha-f) (vla-5) (cd49e). [swissprot;acc:p08648] Squared Divided Low confidence 57397.4 53011.1 1.08274
jagged 2 precursor (jagged2) (hj2). [swissprot;acc:q9y219] Rooted Subtracted 66.0188 69.7871 3.7683
kv channel interacting protein 2 isoform 4; a-type potassium channel modulatory protein 2; cardiac voltage gated potassium channel modulatory subunit. [refseq;acc:nm_173193] Ranked 213.976 222.312 8.336
large neutral amino acids transporter small subunit 2 (l-type amino acid transporter 2) (hlat2). [swissprot;acc:q9uhi5] Divided 205.154 196.72 1.04287
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] Rooted High confidence 203.673 182.638 1.11517
melanoma antigen, family d, 4 isoform 1; mage1 protein; mage-e1 protein; maged4 protein. [refseq;acc:nm_030801] Ranked Subtracted 88.2482 110.265 22.0168
nucleolar protein family a, member 1; gar1 protein. [refseq;acc:nm_018983] Measured 4446.72 5553.79 1107.07
prefoldin subunit 1. [swissprot;acc:o60925] Rooted Divided Low confidence 70.2592 74.0161 1.05347
proto-oncogene tyrosine-protein kinase src (ec 2.7.1.112) (p60-src) (c-src). [swissprot;acc:p12931] Squared High confidence 28896.2 36767 1.27238
302 60s ribosomal protein l26. [swissprot;acc:q02877] Ranked 242.326 267.008 1.10185
coatomer delta subunit (delta-coat protein) (delta-cop) (archain). [swissprot;acc:p48444] Squared Subtracted 51527.6 43689.1 7838.5
cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438] Rooted Divided 203.673 182.638 1.11517
dual oxidase 1 precursor; nadph thyroid oxidase 1; flavoprotein nadph oxidase; nicotinamide adenine dinucleotide phosphate oxidase. [refseq;acc:nm_017434] Measured Subtracted Low confidence 7900.92 8375.39 474.47
hepatocellular carcinoma-associated protein hca3. [refseq;acc:nm_138703] Ranked High confidence 88.2482 110.265 22.0168
homeobox protein cux-2 (cut-like 2) (fragment). [swissprot;acc:o14529] Rooted 66.1046 74.0964 7.9918
integrin alpha-v precursor (vitronectin receptor alpha subunit) (cd51 antigen). [swissprot;acc:p06756] Squared Divided Low confidence 57397.4 53011.1 1.08274
mothers against decapentaplegic homolog 2 (smad 2) (mothers against dpp homolog 2) (mad-related protein 2) (hmad-2) (jv18-1) (hsmad2). [swissprot;acc:q15796] Subtracted 48958.6 45174.5 3784.1
myocyte-specific enhancer factor 2a (serum response factor-like protein 1). [swissprot;acc:q02078] Rooted 66.0188 69.7871 3.7683
pallidin; pallid (mouse) homolog, pallidin. [refseq;acc:nm_012388] Measured Divided High confidence 5894.75 7073.65 1.19999
potassium voltage-gated channel subfamily a member 2 (potassium channel kv1.2) (rbk2) (hbk5) (ngk1) (mk2) (hukiv). [swissprot;acc:p16389] Ranked Subtracted Low confidence 209.583 201.251 8.332
ribonucleoside-diphosphate reductase m2 chain (ec 1.17.4.1) (ribonucleotide reductase small chain). [swissprot;acc:p31350] Measured High confidence 6704.44 7811.45 1107.01
secreted modular calcium-binding protein 2; smooth muscle associated protein 2. [refseq;acc:nm_022138] Rooted Divided Low confidence 70.2592 74.0161 1.05347
tfiih basal transcription factor complex p34 subunit (basic transcription factor 2 34 kda subunit) (btf2-p34) (general transcription factor iih polypeptide 3). [swissprot;acc:q13889] Measured 9243.98 9781.77 1.05818
tyrosine-protein kinase hck (ec 2.7.1.112) (p59-hck/p60-hck) (hemopoietic cell kinase). [swissprot;acc:p08631] Squared High confidence 28896.2 36767 1.27238
xenotropic and polytropic retrovirus receptor. [refseq;acc:nm_004736] Ranked Low confidence 209.12 200.548 1.04274
303 60s ribosomal protein l35. [swissprot;acc:p42766] High confidence 242.333 266.999 1.10179
choline dehydrogenase. [refseq;acc:nm_018397] Rooted Low confidence 70.2592 74.0161 1.05347
crk-like protein. [swissprot;acc:p46109] Squared High confidence 28896.2 36767 1.27238
cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418] Rooted 203.673 182.638 1.11517
diacylglycerol o-acyltransferase 1 (ec 2.3.1.20) (diglyceride acyltransferase) (acat related gene product 1). [swissprot;acc:o75907] Measured Subtracted Low confidence 7902.9 8376.6 473.7
homeobox protein nkx-6.1. [swissprot;acc:p78426] Divided 9810.95 10381.3 1.05813
homer, neuronal immediate early gene, 3. [refseq;acc:nm_004838] Ranked 210.057 201.45 1.04273
integrin alpha-8. [swissprot;acc:p53708] Squared 57397.4 53011.1 1.08274
melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [swissprot;acc:p43357] Ranked Subtracted High confidence 88.2482 110.265 22.0168
myocyte-specific enhancer factor 2d. [swissprot;acc:q14814] Rooted Low confidence 66.0196 69.7878 3.7682
peptidyl-prolyl cis-trans isomerase e (ec 5.2.1.8) (ppiase e) (rotamase e) (cyclophilin e) (cyclophilin 33). [swissprot;acc:q9unp9] Squared High confidence 51527.6 43689.1 7838.5
potassium voltage-gated channel subfamily a member 1 (potassium channel kv1.1) (huki) (hbk1). [swissprot;acc:q09470] Ranked Low confidence 209.58 201.251 8.329
ribonucleoside-diphosphate reductase m2 chain (ec 1.17.4.1) (ribonucleotide reductase small chain). [swissprot;acc:p31350] Rooted High confidence 62.9007 70.8854 7.9847
serine/threonine protein phosphatase pp1-gamma catalytic subunit (ec 3.1.3.16) (pp-1g). [swissprot;acc:p36873] Measured Divided 22268.8 18560.4 1.1998
spliceosomal u5 snrnp-specific 15 kda protein (dim1 protein homolog) (thioredoxin-like u5 snrnp protein u5-15kd). [swissprot;acc:o14834] Subtracted 4723.53 5828.46 1104.93
wd-repeat protein an11 homolog. [swissprot;acc:o15491] Squared Low confidence 49674.5 45895.5 3779
304 40s ribosomal protein s15 (rig protein). [swissprot;acc:p11174] Ranked Divided High confidence 242.339 266.986 1.1017
coatomer zeta-2 subunit (zeta-2 coat protein) (zeta-2 cop). [swissprot;acc:q9p299] Squared Subtracted 51527.6 43689.1 7838.5
cytohesin 4. [swissprot;acc:q9uia0] Rooted Divided 203.673 182.638 1.11517
integrin alpha-iib precursor (platelet membrane glycoprotein iib) (gpalpha iib) (gpiib) (cd41 antigen). [swissprot;acc:p08514] Squared Low confidence 57397.4 53011.1 1.08274
jagged 1 precursor (jagged1) (hj1). [swissprot;acc:p78504] Rooted Subtracted 66.0195 69.7877 3.7682
kh domain containing, rna binding, signal transduction associated 1; gap-associated tyrosine phosphoprotein p62 (sam68). [refseq;acc:nm_006559] Ranked Divided 209.232 200.662 1.04271
melanoma-associated antigen 11 (mage-11 antigen). [swissprot;acc:p43364] Subtracted High confidence 88.2482 110.265 22.0168
nadph oxidase, ef hand calcium-binding domain 5. [refseq;acc:nm_024505] Measured Low confidence 7904.14 8377.35 473.21
nk6 transcription factor related, locus 2; nk homeobox family 6, b; glial and testis-specific homeobox protein; homeobox 6b. [refseq;acc:nm_177400] Divided 9810.95 10381.3 1.05813

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/