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