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 description Gene Hugo Network Comparison Type Value Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 25 to 74 of 16578 in total
Value Type  : Ranked
Filtered  : 1
Rank
description
Hugo
Network Comparison Type
Interaction Map
red
green
network_comparison
7 homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774] HLX Divided High confidence 215 322 1.49767
oxysterol binding protein-related protein 3 (osbp-related protein 3) (orp-3). [swissprot;acc:q9h4l5] OSBPL3 Low confidence 318 240 1.325
oxysterol binding protein-related protein 7 (osbp-related protein 7) (orp-7). [swissprot;acc:q9bzf2] OSBPL7 Subtracted 78
protein cgi-126 (protein hspc155). [swissprot;acc:q9y3c8] UFC1 High confidence 288.754 212.554 76.2
8 hbs1-like. [refseq;acc:nm_006620] HBS1L Divided 215 322 1.49767
junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2] JPH3 Subtracted 288 362 74
oxysterol binding protein-related protein 7 (osbp-related protein 7) (orp-7). [swissprot;acc:q9bzf2] OSBPL7 Divided Low confidence 318 240 1.325
thyroid receptor interacting protein 8 (trip-8) (fragment). [swissprot;acc:q15652] JMJD1C Subtracted 305.472 247.246 58.226
9 28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5] MRPS17 Divided 58 44 1.31818
gbp protein isoform a. [refseq;acc:nm_017870] TMEM132A Subtracted 305.399 247.213 58.186
junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39] JPH2 High confidence 288 362 74
xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [refseq;acc:nm_007266] XAB1 Divided 212 309 1.45755
10 jumonji domain containing 1; zinc finger protein; testis-specific protein a. [refseq;acc:nm_018433] JMJD1A Subtracted Low confidence 305.303 247.169 58.134
mitochondrial solute carrier protein. [refseq;acc:nm_145305] SLC25A43 Divided 58 44 1.31818
protein x 0004. [refseq;acc:nm_016301] ATPBD1C High confidence 212 309 1.45755
sphingomyelin phosphodiesterase 2 (ec 3.1.4.12) (neutral sphingomyelinase) (nsmase) (n-smase) (lyso-platelet activating factor- phospholipase c) (lyso-paf-plc). [swissprot;acc:o60906] SMPD2 Subtracted 288 362 74
11 bestrophin (vitelliform macular dystrophy protein) (tu15b). [swissprot;acc:o76090] BEST1 Divided Low confidence 37.318 28.4944 1.30966
db83 protein. [swissprot;acc:p57088] TMEM33 Subtracted High confidence 288 362 74
rad50-interacting protein 1. [refseq;acc:nm_021930] RINT1 Divided 337 232 1.45259
trypsin iii precursor (ec 3.4.21.4) (brain trypsinogen) (mesotrypsinogen) (trypsin iv). [swissprot;acc:p35030] PRSS3 Subtracted Low confidence 304.548 246.824 57.724
12 guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-7 subunit. [swissprot;acc:o60262] no value High confidence 266.856 336.233 69.377
rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6] RHOBTB2 Divided 337 232 1.45259
trypsin i precursor (ec 3.4.21.4) (cationic trypsinogen). [swissprot;acc:p07477] PRSS1 Subtracted Low confidence 304.359 246.737 57.622
vitelliform macular dystrophy 2-like protein 2. [refseq;acc:nm_153274] BEST4 Divided 37.3475 28.5242 1.30933
13 guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-12 subunit. [swissprot;acc:q9ubi6] GNG12 Subtracted High confidence 266.856 336.233 69.377
nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333] no value Divided Low confidence 37.9984 29.1831 1.30207
protein cgi-126 (protein hspc155). [swissprot;acc:q9y3c8] UFC1 High confidence 288.754 212.554 1.3585
Subtracted Low confidence 255.046 202.362 52.684
14 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] CYP27B1 286.396 238.476 47.92
cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936] ATG4A Divided High confidence 56.6768 75.3531 1.32952
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-4 subunit. [swissprot;acc:p50150] GNG4 Subtracted 266.863 336.191 69.328
vitelliform macular dystrophy 2-like protein 1. [refseq;acc:nm_017682] BEST2 Divided Low confidence 37.9984 29.1831 1.30207
15 cytochrome p450 27, mitochondrial precursor (ec 1.14.-.-) (cytochrome p-450c27/25) (sterol 26-hydroxylase) (sterol 27-hydroxylase) (vitamin d(3) 25-hydroxylase) (5-beta-cholestane-3-alpha,7-alpha,12-alpha-triol 27-hydroxylase). [swissprot;acc:q02318] CYP27A1 Subtracted 286.347 238.454 47.893
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-3 subunit. [swissprot;acc:p29798] GNG3 High confidence 266.863 336.19 69.327
microtubule-associated proteins 1a/1b light chain 3b (map1a/map1b lc3 b) (map1a/1b light chain 3 b). [swissprot;acc:q9gzq8] MAP1LC3B Divided 56.7244 75.3948 1.32914
protein cgi-126 (protein hspc155). [swissprot;acc:q9y3c8] UFC1 Low confidence 255.046 202.362 1.26035
16 cytochrome p450 24a1, mitochondrial precursor (ec 1.14.-.-) (p450- cc24) (vitamin d(3) 24-hydroxylase) (1,25-dihydroxyvitamin d(3) 24- hydroxylase) (24-ohase). [swissprot;acc:q07973] CYP24A1 Subtracted 284.798 237.743 47.055
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-8 subunit (gamma-9). [swissprot;acc:q9uk08] GNG8 High confidence 266.864 336.184 69.32
microtubule-associated proteins 1a/1b light chain 3a (map1a/map1b lc3 a) (map1a/1b light chain 3 a). [swissprot;acc:q9h492] MAP1LC3A Divided 56.7252 75.3954 1.32913
thyroid receptor interacting protein 8 (trip-8) (fragment). [swissprot;acc:q15652] JMJD1C Low confidence 305.472 247.246 1.2355
17 bcl2-related ovarian killer. [refseq;acc:nm_032515] BOK Subtracted 265.638 223.235 42.403
cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326] ATG4B Divided High confidence 56.7841 75.447 1.32866
gbp protein isoform a. [refseq;acc:nm_017870] TMEM132A Low confidence 305.399 247.213 1.23537
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 subunit. [swissprot;acc:p30670] GNG5 Subtracted High confidence 266.864 336.182 69.318
18 1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446] GBE1 Divided 185.678 245.247 1.32082
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-10 subunit. [swissprot;acc:p50151] GNG10 Subtracted 266.865 336.181 69.316
jumonji domain containing 1; zinc finger protein; testis-specific protein a. [refseq;acc:nm_018433] JMJD1A Divided Low confidence 305.303 247.169 1.2352
protein kinase, interferon-inducible double stranded rna dependent activator; protein activator of the interferon-induced protein kinase. [refseq;acc:nm_003690] PRKRAP1 Subtracted 273.188 232.49 40.698
19 glycogen phosphorylase, brain form (ec 2.4.1.1). [swissprot;acc:p11216] PYGB Divided High confidence 185.678 245.247 1.32082
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 like subunit. [swissprot;acc:q9y3k8] no value Subtracted 266.865 336.178 69.313

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
- Hugo is the HGNC identifier if it exists
- 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/