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 Network Comparison Type Gene Value Type description Interaction Map green red Filtered network_comparison
Results: HTML CSV LaTeX Showing element 451 to 500 of 16578 in total
Value Type  : Measured
Filtered  : 1
Rank
Network Comparison Type
description
Interaction Map
green
red
network_comparison
113 Subtracted cyclic-amp-dependent transcription factor atf-3 (activating transcription factor 3). [swissprot;acc:p18847] High confidence 7132.71 4800.81 2331.9
monocarboxylate transporter 1 (mct 1). [swissprot;acc:p53985] Low confidence 11206.7 10348.5 858.2
114 Divided huntingtin interacting protein c. [refseq;acc:nm_012272] High confidence 5807.72 4300.47 1.35048
melanoma-associated antigen 11 (mage-11 antigen). [swissprot;acc:p43364] Low confidence 10318.5 11285.3 1.0937
Subtracted cyclin-dependent kinases regulatory subunit 1 (cks-1) (sid1334) (pnas-16 / pnas-143). [swissprot;acc:p33551] High confidence 11466 13768.2 2302.2
monocarboxylate transporter 2 (mct 2). [swissprot;acc:o60669] Low confidence 11204.8 10346.9 857.9
115 Divided 28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5] High confidence 28492 21185 1.34491
melanoma-associated antigen 2 (mage-2 antigen). [swissprot;acc:p43356] Low confidence 10318.5 11285.3 1.0937
Subtracted monocarboxylate transporter 3 (mct 3). [swissprot;acc:o95907] 11198.5 10341.7 856.8
pnas-18. [sptrembl;acc:q9bzu3] High confidence 11409.6 13680.5 2270.9
116 Divided hepatocellular carcinoma-associated protein hca1. [refseq;acc:nm_020932] Low confidence 10318.5 11285.3 1.0937
pantothenate kinase 1 (ec 2.7.1.33) (pantothenic acid kinase 1) (hpank1) (hpank). [swissprot;acc:q8te04] High confidence 28492 21185 1.34491
Subtracted amino acid transporter xat2; likely ortholog of mouse aspartate/glutamate transporter 1 (agt1). [refseq;acc:nm_138817] Low confidence 7848.45 6991.78 856.67
ral guanine nucleotide dissociation stimulator-like 1 (ralgds-like 1). [swissprot;acc:q9nzl6] High confidence 11017.8 13261.9 2244.1
117 Divided melanoma-associated antigen 6 (mage-6 antigen) (mage3b). [swissprot;acc:p43360] Low confidence 10318.5 11285.3 1.0937
pantothenate kinase 2, mitochondrial precursor (ec 2.7.1.33) (pantothenic acid kinase 2) (hpank2). [swissprot;acc:q9bz23] High confidence 28492 21185 1.34491
Subtracted metalloprotease 1; metalloprotease 1 (pitrilysin family). [refseq;acc:nm_014889] 7090.37 9276.47 2186.1
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] Low confidence 7848.45 6991.78 856.67
118 Divided necdin. [swissprot;acc:q99608] 10318.5 11285.3 1.0937
pantothenate kinase 3 (ec 2.7.1.33) (pantothenic acid kinase 3) (hpank3). [swissprot;acc:q9h999] High confidence 28492 21185 1.34491
Subtracted beta-1,4 mannosyltransferase. [refseq;acc:nm_019109] 7089.65 9275.1 2185.45
cystine/glutamate transporter (amino acid transport system xc-) (xct) (calcium channel blocker resistance protein ccbr1). [swissprot;acc:q9upy5] Low confidence 7848.45 6991.78 856.67
119 Divided melanoma-associated antigen d1 (mage-d1 antigen) (neurotrophin receptor-interacting mage homolog) (pro2292). [swissprot;acc:q9y5v3] 10318.5 11285.3 1.0937
mitochondrial solute carrier protein. [refseq;acc:nm_145305] High confidence 28492 21185 1.34491
Subtracted acyl-coa dehydrogenase, very-long-chain specific, mitochondrial precursor (ec 1.3.99.-) (vlcad). [swissprot;acc:p49748] 15138.2 12998.5 2139.7
solute carrier family 7 (cationic amino acid transporter, y+ system), member 6. [refseq;acc:nm_003983] Low confidence 7848.45 6991.78 856.67
120 Divided 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] High confidence 6895.98 5136.78 1.34247
melanoma-associated antigen f1 (mage-f1 antigen). [swissprot;acc:q9hay2] Low confidence 10318.5 11285.3 1.0937
Subtracted eukaryotic translation initiation factor 4b (eif-4b). [swissprot;acc:p23588] 7848.45 6991.78 856.67
proto-oncogene protein c-fos (cellular oncogene fos) (g0/g1 switch regulatory protein 7). [swissprot;acc:p01100] High confidence 7033.29 4932.27 2101.02
121 Divided melanoma antigen, family b, 6. [refseq;acc:nm_173523] Low confidence 10318.5 11285.3 1.0937
transcription factor jun-b. [swissprot;acc:p17275] High confidence 7488.4 5579.18 1.3422
Subtracted b(0,+)-type amino acid transporter 1 (b(0,+)at) (glycoprotein- associated amino acid transporter b0,+at1). [swissprot;acc:p82251] Low confidence 7848.45 6991.78 856.67
jun dimerization protein. [refseq;acc:nm_130469] High confidence 7033.29 4932.27 2101.02
122 Divided high-mobility group 20a. [refseq;acc:nm_018200] 6893.53 5140.14 1.34112
melanoma-associated antigen 4 (mage-4 antigen) (mage-x2) (mage-41). [swissprot;acc:p43358] Low confidence 10318.5 11285.3 1.0937
Subtracted fos-related antigen 2. [swissprot;acc:p15408] High confidence 7037.11 4941.95 2095.16
monocarboxylate transporter 4 (mct 4) (mct 3). [swissprot;acc:o15427] Low confidence 11178.2 10325 853.2
123 Divided cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936] High confidence 18172.1 24260.3 1.33503
melanoma-associated antigen 9 (mage-9 antigen). [swissprot;acc:p43362] Low confidence 10318.5 11285.3 1.0937
Subtracted protein fosb (g0/g1 switch regulatory protein 3). [swissprot;acc:p53539] High confidence 7037.32 4942.49 2094.83
transmembrane protein tmp21 precursor (21 kda transmembrane trafficking protein) (p24delta) (s31iii125) (s31i125) (tmp-21-i). [swissprot;acc:p49755] Low confidence 12252.1 11403 849.1
124 Divided melanoma-associated antigen 8 (mage-8 antigen). [swissprot;acc:p43361] 10318.5 11285.3 1.0937
microtubule-associated proteins 1a/1b light chain 3b (map1a/map1b lc3 b) (map1a/1b light chain 3 b). [swissprot;acc:q9gzq8] High confidence 18168.9 24255.7 1.33501
Subtracted fos-related antigen 1 (fra-1). [swissprot;acc:p15407] 7038.04 4944.3 2093.74
phosphatidylinositol glycan, class b. [refseq;acc:nm_004855] Low confidence 12252.1 11403 849.1
125 Divided melanoma-associated antigen c1 (mage-c1 antigen) (cancer-testis antigen ct7). [swissprot;acc:o60732] 10318.5 11285.3 1.0937
microtubule-associated proteins 1a/1b light chain 3a (map1a/map1b lc3 a) (map1a/1b light chain 3 a). [swissprot;acc:q9h492] High confidence 18168.9 24255.7 1.33501
Subtracted hira-interacting protein 5 (cgi-33). [swissprot;acc:q9ums0] 14561.7 12471.7 2090
septin 2 (nedd5 protein homolog). [swissprot;acc:q15019] Low confidence 10996.7 10168.5 828.2

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/