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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Value Type Interaction Map Gene Rank Network Comparison Type Filtered description green red network_comparison
Results: HTML CSV LaTeX Showing element 451 to 500 of 29840 in total
Value Type  : Measured
Interaction Map  : High confidence
Rank
Network Comparison Type
Filtered
description
green
red
network_comparison
113 Subtracted 0 transcription factor cp2; transcription factor cp2, alpha globin. [refseq;acc:nm_005653] 2833.94 3117.17 283.23
1 cyclic-amp-dependent transcription factor atf-3 (activating transcription factor 3). [swissprot;acc:p18847] 7132.71 4800.81 2331.9
114 Divided 0 daz associated protein 1 isoform b; deleted in azoospermia associated protein 1. [refseq;acc:nm_018959] 472.945 671.769 1.4204
1 huntingtin interacting protein c. [refseq;acc:nm_012272] 5807.72 4300.47 1.35048
Subtracted 0 60s ribosomal protein l37a. [swissprot;acc:p12751] 26.1599 305.45 279.29
1 cyclin-dependent kinases regulatory subunit 1 (cks-1) (sid1334) (pnas-16 / pnas-143). [swissprot;acc:p33551] 11466 13768.2 2302.2
115 Divided 0 zinc finger protein-like 1; zinc-finger protein in men1 region. [refseq;acc:nm_006782] 543 385 1.41039
1 28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5] 28492 21185 1.34491
Subtracted 0 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] 26.1599 305.45 279.29
1 pnas-18. [sptrembl;acc:q9bzu3] 11409.6 13680.5 2270.9
116 Divided 0 alpha-parvin (calponin-like integrin-linked kinase binding protein) (ch-ilkbp). [swissprot;acc:q9nvd7] 475 668 1.40632
1 pantothenate kinase 1 (ec 2.7.1.33) (pantothenic acid kinase 1) (hpank1) (hpank). [swissprot;acc:q8te04] 28492 21185 1.34491
Subtracted 0 cylindromatosis (turban tumor syndrome); cylindromatosis 1, turban tumor syndrome. [refseq;acc:nm_015247] 1107 1382.5 275.5
1 ral guanine nucleotide dissociation stimulator-like 1 (ralgds-like 1). [swissprot;acc:q9nzl6] 11017.8 13261.9 2244.1
117 Divided 0 ubiquitin activating enzyme e1-like protein. [refseq;acc:nm_006395] 122 170.5 1.39754
1 pantothenate kinase 2, mitochondrial precursor (ec 2.7.1.33) (pantothenic acid kinase 2) (hpank2). [swissprot;acc:q9bz23] 28492 21185 1.34491
Subtracted 0 ccr4-not transcription complex, subunit 7 (ccr4-associated factor 1) (caf1) (btg1 binding factor 1). [swissprot;acc:q9uiv1] 891.114 1161.88 270.766
1 metalloprotease 1; metalloprotease 1 (pitrilysin family). [refseq;acc:nm_014889] 7090.37 9276.47 2186.1
118 Divided 0 methyltransferase like 2. [refseq;acc:nm_018396] 43 31 1.3871
1 pantothenate kinase 3 (ec 2.7.1.33) (pantothenic acid kinase 3) (hpank3). [swissprot;acc:q9h999] 28492 21185 1.34491
Subtracted 0 glutathione s-transferase theta 2 (ec 2.5.1.18) (gst class-theta). [swissprot;acc:p30712] 593.094 324.442 268.652
1 beta-1,4 mannosyltransferase. [refseq;acc:nm_019109] 7089.65 9275.1 2185.45
119 Divided 0 estrogen-related receptor gamma (estrogen receptor related protein 3) (err gamma-2). [swissprot;acc:o75454] 460.2 633.85 1.37734
1 mitochondrial solute carrier protein. [refseq;acc:nm_145305] 28492 21185 1.34491
Subtracted 0 ubiquitin protein ligase. [refseq;acc:nm_130466] 352.75 620 267.25
1 acyl-coa dehydrogenase, very-long-chain specific, mitochondrial precursor (ec 1.3.99.-) (vlcad). [swissprot;acc:p49748] 15138.2 12998.5 2139.7
120 Divided 0 signal-induced proliferation-associated 1-like 1. [refseq;acc:nm_015556] 359.631 494.417 1.37479
1 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] 6895.98 5136.78 1.34247
Subtracted 0 transducin beta-like 2 protein (ws beta-transducin repeats protein) (ws-betatrp) (williams-beuren syndrome chromosome region 13 protein). [swissprot;acc:q9y4p3] 551.434 817.81 266.376
1 proto-oncogene protein c-fos (cellular oncogene fos) (g0/g1 switch regulatory protein 7). [swissprot;acc:p01100] 7033.29 4932.27 2101.02
121 Divided 0 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] 14.3333 19.6667 1.3721
1 transcription factor jun-b. [swissprot;acc:p17275] 7488.4 5579.18 1.3422
Subtracted 0 presenilin-like protein 1 (ec 3.4.99.-) (sppl2b protein). [swissprot;acc:q8tct7] 1139 874 265
1 jun dimerization protein. [refseq;acc:nm_130469] 7033.29 4932.27 2101.02
122 Divided 0 sh2-b homolog; likely ortholog of mouse sh2 domain-containing putative adapter sh2-b; sh2-b gamma signaling protein; sh2-b alpha signaling protein. [refseq;acc:nm_015503] 78 107 1.37179
1 high-mobility group 20a. [refseq;acc:nm_018200] 6893.53 5140.14 1.34112
Subtracted 0 casein kinase i alpha s-like. [refseq;acc:nm_145203] 1933.94 2198.47 264.53
1 fos-related antigen 2. [swissprot;acc:p15408] 7037.11 4941.95 2095.16
123 Divided 0 ret finger protein 2 (leukemia associated protein 5) (b-cell chronic lymphocytic leukemia tumor suppressor leu5) (putative tumor suppressor rfp2) (tripartite motif protein 13). [swissprot;acc:o60858] 1681.3 2285.62 1.35944
1 cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936] 18172.1 24260.3 1.33503
Subtracted 0 putative nucleoside diphosphate kinase (ec 2.7.4.6) (ndk) (ndp kinase). [swissprot;acc:o60361] 1643 1905.84 262.84
1 protein fosb (g0/g1 switch regulatory protein 3). [swissprot;acc:p53539] 7037.32 4942.49 2094.83
124 Divided 0 regulator of chromosome condensation (cell cycle regulatory protein). [swissprot;acc:p18754] 2399.76 3248.95 1.35386
1 microtubule-associated proteins 1a/1b light chain 3b (map1a/map1b lc3 b) (map1a/1b light chain 3 b). [swissprot;acc:q9gzq8] 18168.9 24255.7 1.33501
Subtracted 0 brain protein 16. [refseq;acc:nm_016458] 2418.14 2155.75 262.39
1 fos-related antigen 1 (fra-1). [swissprot;acc:p15407] 7038.04 4944.3 2093.74
125 Divided 0 probable calcium-transporting atpase kiaa0703 (ec 3.6.3.8). [swissprot;acc:o75185] 812.166 1095.42 1.34876
1 microtubule-associated proteins 1a/1b light chain 3a (map1a/map1b lc3 a) (map1a/1b light chain 3 a). [swissprot;acc:q9h492] 18168.9 24255.7 1.33501
Subtracted 0 glutamate dehydrogenase 2, mitochondrial precursor (ec 1.4.1.3) (gdh). [swissprot;acc:p49448] 3952.59 3691.15 261.44
1 hira-interacting protein 5 (cgi-33). [swissprot;acc:q9ums0] 14561.7 12471.7 2090

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/