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 Gene Rank description Network Comparison Type Interaction Map green red Filtered network_comparison
Results: HTML CSV LaTeX Showing element 451 to 500 of 29840 in total
Value Type  : Measured
Interaction Map  : High confidence
Rank
description
Network Comparison Type
green
red
Filtered
network_comparison
113 sh3 domain-binding glutamic acid-rich-like protein 2 (fovea-associated sh3 domain binding protein). [swissprot;acc:q9ujc5] Divided 112.25 160 0 1.42539
transcription factor cp2; transcription factor cp2, alpha globin. [refseq;acc:nm_005653] Subtracted 2833.94 3117.17 283.23
114 60s ribosomal protein l37a. [swissprot;acc:p12751] 26.1599 305.45 279.29
cyclin-dependent kinases regulatory subunit 1 (cks-1) (sid1334) (pnas-16 / pnas-143). [swissprot;acc:p33551] 11466 13768.2 1 2302.2
daz associated protein 1 isoform b; deleted in azoospermia associated protein 1. [refseq;acc:nm_018959] Divided 472.945 671.769 0 1.4204
huntingtin interacting protein c. [refseq;acc:nm_012272] 5807.72 4300.47 1 1.35048
115 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] Subtracted 26.1599 305.45 0 279.29
28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5] Divided 28492 21185 1 1.34491
pnas-18. [sptrembl;acc:q9bzu3] Subtracted 11409.6 13680.5 2270.9
zinc finger protein-like 1; zinc-finger protein in men1 region. [refseq;acc:nm_006782] Divided 543 385 0 1.41039
116 alpha-parvin (calponin-like integrin-linked kinase binding protein) (ch-ilkbp). [swissprot;acc:q9nvd7] 475 668 1.40632
cylindromatosis (turban tumor syndrome); cylindromatosis 1, turban tumor syndrome. [refseq;acc:nm_015247] Subtracted 1107 1382.5 275.5
pantothenate kinase 1 (ec 2.7.1.33) (pantothenic acid kinase 1) (hpank1) (hpank). [swissprot;acc:q8te04] Divided 28492 21185 1 1.34491
ral guanine nucleotide dissociation stimulator-like 1 (ralgds-like 1). [swissprot;acc:q9nzl6] Subtracted 11017.8 13261.9 2244.1
117 ccr4-not transcription complex, subunit 7 (ccr4-associated factor 1) (caf1) (btg1 binding factor 1). [swissprot;acc:q9uiv1] 891.114 1161.88 0 270.766
metalloprotease 1; metalloprotease 1 (pitrilysin family). [refseq;acc:nm_014889] 7090.37 9276.47 1 2186.1
pantothenate kinase 2, mitochondrial precursor (ec 2.7.1.33) (pantothenic acid kinase 2) (hpank2). [swissprot;acc:q9bz23] Divided 28492 21185 1.34491
ubiquitin activating enzyme e1-like protein. [refseq;acc:nm_006395] 122 170.5 0 1.39754
118 beta-1,4 mannosyltransferase. [refseq;acc:nm_019109] Subtracted 7089.65 9275.1 1 2185.45
glutathione s-transferase theta 2 (ec 2.5.1.18) (gst class-theta). [swissprot;acc:p30712] 593.094 324.442 0 268.652
methyltransferase like 2. [refseq;acc:nm_018396] Divided 43 31 1.3871
pantothenate kinase 3 (ec 2.7.1.33) (pantothenic acid kinase 3) (hpank3). [swissprot;acc:q9h999] 28492 21185 1 1.34491
119 acyl-coa dehydrogenase, very-long-chain specific, mitochondrial precursor (ec 1.3.99.-) (vlcad). [swissprot;acc:p49748] Subtracted 15138.2 12998.5 2139.7
estrogen-related receptor gamma (estrogen receptor related protein 3) (err gamma-2). [swissprot;acc:o75454] Divided 460.2 633.85 0 1.37734
mitochondrial solute carrier protein. [refseq;acc:nm_145305] 28492 21185 1 1.34491
ubiquitin protein ligase. [refseq;acc:nm_130466] Subtracted 352.75 620 0 267.25
120 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 6895.98 5136.78 1 1.34247
proto-oncogene protein c-fos (cellular oncogene fos) (g0/g1 switch regulatory protein 7). [swissprot;acc:p01100] Subtracted 7033.29 4932.27 2101.02
signal-induced proliferation-associated 1-like 1. [refseq;acc:nm_015556] Divided 359.631 494.417 0 1.37479
transducin beta-like 2 protein (ws beta-transducin repeats protein) (ws-betatrp) (williams-beuren syndrome chromosome region 13 protein). [swissprot;acc:q9y4p3] Subtracted 551.434 817.81 266.376
121 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] Divided 14.3333 19.6667 1.3721
jun dimerization protein. [refseq;acc:nm_130469] Subtracted 7033.29 4932.27 1 2101.02
presenilin-like protein 1 (ec 3.4.99.-) (sppl2b protein). [swissprot;acc:q8tct7] 1139 874 0 265
transcription factor jun-b. [swissprot;acc:p17275] Divided 7488.4 5579.18 1 1.3422
122 casein kinase i alpha s-like. [refseq;acc:nm_145203] Subtracted 1933.94 2198.47 0 264.53
fos-related antigen 2. [swissprot;acc:p15408] 7037.11 4941.95 1 2095.16
high-mobility group 20a. [refseq;acc:nm_018200] Divided 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] 78 107 0 1.37179
123 cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936] 18172.1 24260.3 1 1.33503
protein fosb (g0/g1 switch regulatory protein 3). [swissprot;acc:p53539] Subtracted 7037.32 4942.49 2094.83
putative nucleoside diphosphate kinase (ec 2.7.4.6) (ndk) (ndp kinase). [swissprot;acc:o60361] 1643 1905.84 0 262.84
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] Divided 1681.3 2285.62 1.35944
124 brain protein 16. [refseq;acc:nm_016458] Subtracted 2418.14 2155.75 262.39
fos-related antigen 1 (fra-1). [swissprot;acc:p15407] 7038.04 4944.3 1 2093.74
microtubule-associated proteins 1a/1b light chain 3b (map1a/map1b lc3 b) (map1a/1b light chain 3 b). [swissprot;acc:q9gzq8] Divided 18168.9 24255.7 1.33501
regulator of chromosome condensation (cell cycle regulatory protein). [swissprot;acc:p18754] 2399.76 3248.95 0 1.35386
125 glutamate dehydrogenase 2, mitochondrial precursor (ec 1.4.1.3) (gdh). [swissprot;acc:p49448] Subtracted 3952.59 3691.15 261.44
hira-interacting protein 5 (cgi-33). [swissprot;acc:q9ums0] 14561.7 12471.7 1 2090
microtubule-associated proteins 1a/1b light chain 3a (map1a/map1b lc3 a) (map1a/1b light chain 3 a). [swissprot;acc:q9h492] Divided 18168.9 24255.7 1.33501
probable calcium-transporting atpase kiaa0703 (ec 3.6.3.8). [swissprot;acc:o75185] 812.166 1095.42 0 1.34876

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/