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 Network Comparison Type Value Type Interaction Map Filtered network_comparison green red
Results: HTML CSV LaTeX Showing element 451 to 500 of 16578 in total
Value Type  : Measured
Filtered  : 1
Rank
description
Network Comparison Type
Interaction Map
network_comparison
green
red
113 melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [swissprot;acc:p43357] Divided Low confidence 1.0937 10318.5 11285.3
monocarboxylate transporter 1 (mct 1). [swissprot;acc:p53985] Subtracted 858.2 11206.7 10348.5
114 cyclin-dependent kinases regulatory subunit 1 (cks-1) (sid1334) (pnas-16 / pnas-143). [swissprot;acc:p33551] High confidence 2302.2 11466 13768.2
huntingtin interacting protein c. [refseq;acc:nm_012272] Divided 1.35048 5807.72 4300.47
melanoma-associated antigen 11 (mage-11 antigen). [swissprot;acc:p43364] Low confidence 1.0937 10318.5 11285.3
monocarboxylate transporter 2 (mct 2). [swissprot;acc:o60669] Subtracted 857.9 11204.8 10346.9
115 28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5] Divided High confidence 1.34491 28492 21185
melanoma-associated antigen 2 (mage-2 antigen). [swissprot;acc:p43356] Low confidence 1.0937 10318.5 11285.3
monocarboxylate transporter 3 (mct 3). [swissprot;acc:o95907] Subtracted 856.8 11198.5 10341.7
pnas-18. [sptrembl;acc:q9bzu3] High confidence 2270.9 11409.6 13680.5
116 amino acid transporter xat2; likely ortholog of mouse aspartate/glutamate transporter 1 (agt1). [refseq;acc:nm_138817] Low confidence 856.67 7848.45 6991.78
hepatocellular carcinoma-associated protein hca1. [refseq;acc:nm_020932] Divided 1.0937 10318.5 11285.3
pantothenate kinase 1 (ec 2.7.1.33) (pantothenic acid kinase 1) (hpank1) (hpank). [swissprot;acc:q8te04] High confidence 1.34491 28492 21185
ral guanine nucleotide dissociation stimulator-like 1 (ralgds-like 1). [swissprot;acc:q9nzl6] Subtracted 2244.1 11017.8 13261.9
117 melanoma-associated antigen 6 (mage-6 antigen) (mage3b). [swissprot;acc:p43360] Divided Low confidence 1.0937 10318.5 11285.3
metalloprotease 1; metalloprotease 1 (pitrilysin family). [refseq;acc:nm_014889] Subtracted High confidence 2186.1 7090.37 9276.47
pantothenate kinase 2, mitochondrial precursor (ec 2.7.1.33) (pantothenic acid kinase 2) (hpank2). [swissprot;acc:q9bz23] Divided 1.34491 28492 21185
y+l amino acid transporter 1 (y(+)l-type amino acid transporter 1) (y+lat-1) (y+lat1) (monocyte amino acid permease 2) (mop-2). [swissprot;acc:q9um01] Subtracted Low confidence 856.67 7848.45 6991.78
118 beta-1,4 mannosyltransferase. [refseq;acc:nm_019109] High confidence 2185.45 7089.65 9275.1
cystine/glutamate transporter (amino acid transport system xc-) (xct) (calcium channel blocker resistance protein ccbr1). [swissprot;acc:q9upy5] Low confidence 856.67 7848.45 6991.78
necdin. [swissprot;acc:q99608] Divided 1.0937 10318.5 11285.3
pantothenate kinase 3 (ec 2.7.1.33) (pantothenic acid kinase 3) (hpank3). [swissprot;acc:q9h999] High confidence 1.34491 28492 21185
119 acyl-coa dehydrogenase, very-long-chain specific, mitochondrial precursor (ec 1.3.99.-) (vlcad). [swissprot;acc:p49748] Subtracted 2139.7 15138.2 12998.5
melanoma-associated antigen d1 (mage-d1 antigen) (neurotrophin receptor-interacting mage homolog) (pro2292). [swissprot;acc:q9y5v3] Divided Low confidence 1.0937 10318.5 11285.3
mitochondrial solute carrier protein. [refseq;acc:nm_145305] High confidence 1.34491 28492 21185
solute carrier family 7 (cationic amino acid transporter, y+ system), member 6. [refseq;acc:nm_003983] Subtracted Low confidence 856.67 7848.45 6991.78
120 eukaryotic translation initiation factor 4b (eif-4b). [swissprot;acc:p23588]
high-mobility group 20b; sox-like transcriptional factor; swi/snf-related matrix-associated actin-dependent regulator of chromatin subfamily e, member 1-related. [refseq;acc:nm_006339] Divided High confidence 1.34247 6895.98 5136.78
melanoma-associated antigen f1 (mage-f1 antigen). [swissprot;acc:q9hay2] Low confidence 1.0937 10318.5 11285.3
proto-oncogene protein c-fos (cellular oncogene fos) (g0/g1 switch regulatory protein 7). [swissprot;acc:p01100] Subtracted High confidence 2101.02 7033.29 4932.27
121 b(0,+)-type amino acid transporter 1 (b(0,+)at) (glycoprotein- associated amino acid transporter b0,+at1). [swissprot;acc:p82251] Low confidence 856.67 7848.45 6991.78
jun dimerization protein. [refseq;acc:nm_130469] High confidence 2101.02 7033.29 4932.27
melanoma antigen, family b, 6. [refseq;acc:nm_173523] Divided Low confidence 1.0937 10318.5 11285.3
transcription factor jun-b. [swissprot;acc:p17275] High confidence 1.3422 7488.4 5579.18
122 fos-related antigen 2. [swissprot;acc:p15408] Subtracted 2095.16 7037.11 4941.95
high-mobility group 20a. [refseq;acc:nm_018200] Divided 1.34112 6893.53 5140.14
melanoma-associated antigen 4 (mage-4 antigen) (mage-x2) (mage-41). [swissprot;acc:p43358] Low confidence 1.0937 10318.5 11285.3
monocarboxylate transporter 4 (mct 4) (mct 3). [swissprot;acc:o15427] Subtracted 853.2 11178.2 10325
123 cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936] Divided High confidence 1.33503 18172.1 24260.3
melanoma-associated antigen 9 (mage-9 antigen). [swissprot;acc:p43362] Low confidence 1.0937 10318.5 11285.3
protein fosb (g0/g1 switch regulatory protein 3). [swissprot;acc:p53539] Subtracted High confidence 2094.83 7037.32 4942.49
transmembrane protein tmp21 precursor (21 kda transmembrane trafficking protein) (p24delta) (s31iii125) (s31i125) (tmp-21-i). [swissprot;acc:p49755] Low confidence 849.1 12252.1 11403
124 fos-related antigen 1 (fra-1). [swissprot;acc:p15407] High confidence 2093.74 7038.04 4944.3
melanoma-associated antigen 8 (mage-8 antigen). [swissprot;acc:p43361] Divided Low confidence 1.0937 10318.5 11285.3
microtubule-associated proteins 1a/1b light chain 3b (map1a/map1b lc3 b) (map1a/1b light chain 3 b). [swissprot;acc:q9gzq8] High confidence 1.33501 18168.9 24255.7
phosphatidylinositol glycan, class b. [refseq;acc:nm_004855] Subtracted Low confidence 849.1 12252.1 11403
125 hira-interacting protein 5 (cgi-33). [swissprot;acc:q9ums0] High confidence 2090 14561.7 12471.7
melanoma-associated antigen c1 (mage-c1 antigen) (cancer-testis antigen ct7). [swissprot;acc:o60732] Divided Low confidence 1.0937 10318.5 11285.3
microtubule-associated proteins 1a/1b light chain 3a (map1a/map1b lc3 a) (map1a/1b light chain 3 a). [swissprot;acc:q9h492] High confidence 1.33501 18168.9 24255.7
septin 2 (nedd5 protein homolog). [swissprot;acc:q15019] Subtracted Low confidence 828.2 10996.7 10168.5

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/