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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Gene Value Type Filtered description Rank Network Comparison Type network_comparison Interaction Map green red
Results: HTML CSV LaTeX Showing element 1 to 50 of 9634 in total
Value Type  : Ranked
Filtered  : 0
Network Comparison Type  : Divided
description
Rank
network_comparison
Interaction Map
green
red
1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446] 242 1.09822 High confidence 13895.8 15260.6
629 1.02915 Low confidence 13590.3 13205.3
17-beta-hydroxysteroid dehydrogenase type vii-like. [refseq;acc:nm_182829] 627 1.02953 10050.9 10347.7
25-hydroxyvitamin d-1 alpha hydroxylase, mitochondrial precursor (ec 1.14.-.-) (25-ohd-1 alpha-hydroxylase) (25-hydroxyvitamin d3 1- alpha-hydroxylase) (vd3 1a hydroxylase) (p450c1 alpha) (p450vd1- alpha). [swissprot;acc:o15528] 47 1.42943 High confidence 18499.2 12941.7
384 1.08587 Low confidence 14695.2 13533.1
26s proteasome non-atpase regulatory subunit 10 (26s proteasome regulatory subunit p28) (gankyrin). [swissprot;acc:o75832] 379 1.03909 High confidence 10806 11228.4
825 1.00181 Low confidence 11854.2 11832.8
26s proteasome non-atpase regulatory subunit 12 (26s proteasome regulatory subunit p55). [swissprot;acc:o00232] 495 1.00195 High confidence 11748.1 11725.2
665 1.02285 Low confidence 11538 11801.6
3 beta-hydroxysteroid dehydrogenase (fragments). [sptrembl;acc:q9udk8] 299 1.07178 High confidence 11512.3 12338.7
453 Low confidence
3-hydroxyisobutyryl-coenzyme a hydrolase. [refseq;acc:nm_014362] 327 1.05751 High confidence 10466.5 9897.29
501 1.0588 Low confidence 11352.1 10721.7
3-ketoacyl-coa thiolase, peroxisomal precursor (ec 2.3.1.16) (beta- ketothiolase) (acetyl-coa acyltransferase) (peroxisomal 3-oxoacyl- coa thiolase). [swissprot;acc:p09110] 478 1.00854 High confidence 10243.1 10156.4
614 1.03221 Low confidence 10984.2 10641.4
4-aminobutyrate aminotransferase, mitochondrial precursor (ec 2.6.1.19) (gamma-amino-n-butyrate transaminase) (gaba transaminase) (gaba aminotransferase) (gaba-at) (gaba-t). [swissprot;acc:p80404] 369 1.04536 High confidence 19704.7 18849.7
481 1.0617 Low confidence 10788.6 11454.3
40s ribosomal protein s10. [swissprot;acc:p46783] 488 1.06043 13169.5 12419
40s ribosomal protein s12. [swissprot;acc:p25398] 560 1.04588 11494.2 12021.5
40s ribosomal protein s15 (rig protein). [swissprot;acc:p11174] 222 1.10622 High confidence 11013.2 12183
314 1.11195 Low confidence 10922.5 12145.3
40s ribosomal protein s17. [swissprot;acc:p08708] 156 1.14263 13327.2 15228.1
40s ribosomal protein s2 (s4) (llrep3 protein). [swissprot;acc:p15880] 186 1.12672 High confidence 10592.8 11935.1
409 1.0777 Low confidence 10869.8 11714.4
40s ribosomal protein s25. [swissprot;acc:p25111] 102 1.21683 11774.2 9676.12
40s ribosomal protein s26. [swissprot;acc:p02383] 112 1.1982 High confidence 17098 14269.7
524 1.05312 Low confidence 11262.9 10694.8
40s ribosomal protein s27 (metallopan-stimulin 1) (mps-1). [swissprot;acc:p42677] 380 1.0387 High confidence 9936.37 9566.15
619 1.0306 Low confidence 10278.1 9972.93
40s ribosomal protein s28. [swissprot;acc:p25112] 258 1.09459 High confidence 14193.6 12967.1
612 1.03359 Low confidence 11459 11843.9
40s ribosomal protein s29. [swissprot;acc:p30054] 225 1.10378 High confidence 9997.71 11035.3
729 1.0145 Low confidence 10653.8 10808.3
40s ribosomal protein s3a. [swissprot;acc:p49241] 331 1.05644 High confidence 10992.4 10405.1
786 1.00719 Low confidence 13148.4 13242.9
40s ribosomal protein s4, x isoform (single copy abundant mrna protein) (scr10). [swissprot;acc:p12750] 261 1.09259 High confidence 11393.9 12448.9
444 1.0741 Low confidence 11211.6 12042.4
40s ribosomal protein s4, y isoform 2. [swissprot;acc:q8td47] 260 1.0926 High confidence 11392.6 12447.6
445 1.07401 Low confidence 11218 12048.3
40s ribosomal protein sa (p40) (34/67 kda laminin receptor) (colon carcinoma laminin-binding protein) (nem/1chd4) (multidrug resistance- associated protein mgr1-ag). [swissprot;acc:p08865] 298 1.07219 High confidence 12842.5 11977.8
610 1.03404 Low confidence 12541.1 12128.3
5,6-dihydroxyindole-2-carboxylic acid oxidase precursor (ec 1.14.18.-) (dhica oxidase) (tyrosinase-related protein 1) (trp-1) (trp1) (trp) (catalase b) (glycoprotein-75) (melanoma antigen gp75). [swissprot;acc:p17643] 288 1.07517 High confidence 16053 14930.6
432 Low confidence
5-aminolevulinic acid synthase, nonspecific, mitochondrial precursor (ec 2.3.1.37) (delta-aminolevulinate synthase) (delta-ala synthetase) (alas-h). [swissprot;acc:p13196] 412 1.03217 High confidence 8279.69 8546.06
587 1.04001 Low confidence 8945.68 9303.6
60s acidic ribosomal protein p1. [swissprot;acc:p05386] 233 1.1015 High confidence 10560 9586.97
580 1.04154 Low confidence 11301.8 10851
60s ribosomal protein l10 (qm protein) (tumor suppressor qm) (laminin receptor homolog). [swissprot;acc:p27635] 199 1.11721 High confidence 10545.7 11781.8
402 1.08108 Low confidence 10979.9 11870.1
60s ribosomal protein l10a (csa-19). [swissprot;acc:p53025] 397 1.03414 High confidence 9676.53 10006.9

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/