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 Gene Hugo description Network Comparison Type Value Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 30 to 79 of 16578 in total
Value Type  : Ranked
Filtered  : 1
Rank
Hugo
description
Network Comparison Type
Interaction Map
red
green
network_comparison
8 JMJD1C thyroid receptor interacting protein 8 (trip-8) (fragment). [swissprot;acc:q15652] Subtracted Low confidence 305.472 247.246 58.226
JPH3 junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2] High confidence 288 362 74
OSBPL7 oxysterol binding protein-related protein 7 (osbp-related protein 7) (orp-7). [swissprot;acc:q9bzf2] Divided Low confidence 318 240 1.325
9 JPH2 junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39] Subtracted High confidence 288 362 74
MRPS17 28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5] Divided Low confidence 58 44 1.31818
TMEM132A gbp protein isoform a. [refseq;acc:nm_017870] Subtracted 305.399 247.213 58.186
XAB1 xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [refseq;acc:nm_007266] Divided High confidence 212 309 1.45755
10 ATPBD1C protein x 0004. [refseq;acc:nm_016301]
JMJD1A jumonji domain containing 1; zinc finger protein; testis-specific protein a. [refseq;acc:nm_018433] Subtracted Low confidence 305.303 247.169 58.134
SLC25A43 mitochondrial solute carrier protein. [refseq;acc:nm_145305] Divided 58 44 1.31818
SMPD2 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] Subtracted High confidence 288 362 74
11 BEST1 bestrophin (vitelliform macular dystrophy protein) (tu15b). [swissprot;acc:o76090] Divided Low confidence 37.318 28.4944 1.30966
PRSS3 trypsin iii precursor (ec 3.4.21.4) (brain trypsinogen) (mesotrypsinogen) (trypsin iv). [swissprot;acc:p35030] Subtracted 304.548 246.824 57.724
RINT1 rad50-interacting protein 1. [refseq;acc:nm_021930] Divided High confidence 337 232 1.45259
TMEM33 db83 protein. [swissprot;acc:p57088] Subtracted 288 362 74
12 no value guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-7 subunit. [swissprot;acc:o60262] 266.856 336.233 69.377
BEST4 vitelliform macular dystrophy 2-like protein 2. [refseq;acc:nm_153274] Divided Low confidence 37.3475 28.5242 1.30933
PRSS1 trypsin i precursor (ec 3.4.21.4) (cationic trypsinogen). [swissprot;acc:p07477] Subtracted 304.359 246.737 57.622
RHOBTB2 rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6] Divided High confidence 337 232 1.45259
13 no value nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333] Low confidence 37.9984 29.1831 1.30207
GNG12 guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-12 subunit. [swissprot;acc:q9ubi6] Subtracted High confidence 266.856 336.233 69.377
UFC1 protein cgi-126 (protein hspc155). [swissprot;acc:q9y3c8] Divided 288.754 212.554 1.3585
Subtracted Low confidence 255.046 202.362 52.684
14 ATG4A cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936] Divided High confidence 56.6768 75.3531 1.32952
BEST2 vitelliform macular dystrophy 2-like protein 1. [refseq;acc:nm_017682] Low confidence 37.9984 29.1831 1.30207
CYP27B1 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 286.396 238.476 47.92
GNG4 guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-4 subunit. [swissprot;acc:p50150] High confidence 266.863 336.191 69.328
15 CYP27A1 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] Low confidence 286.347 238.454 47.893
GNG3 guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-3 subunit. [swissprot;acc:p29798] High confidence 266.863 336.19 69.327
MAP1LC3B microtubule-associated proteins 1a/1b light chain 3b (map1a/map1b lc3 b) (map1a/1b light chain 3 b). [swissprot;acc:q9gzq8] Divided 56.7244 75.3948 1.32914
UFC1 protein cgi-126 (protein hspc155). [swissprot;acc:q9y3c8] Low confidence 255.046 202.362 1.26035
16 CYP24A1 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] Subtracted 284.798 237.743 47.055
GNG8 guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-8 subunit (gamma-9). [swissprot;acc:q9uk08] High confidence 266.864 336.184 69.32
JMJD1C thyroid receptor interacting protein 8 (trip-8) (fragment). [swissprot;acc:q15652] Divided Low confidence 305.472 247.246 1.2355
MAP1LC3A microtubule-associated proteins 1a/1b light chain 3a (map1a/map1b lc3 a) (map1a/1b light chain 3 a). [swissprot;acc:q9h492] High confidence 56.7252 75.3954 1.32913
17 ATG4B cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326] 56.7841 75.447 1.32866
BOK bcl2-related ovarian killer. [refseq;acc:nm_032515] Subtracted Low confidence 265.638 223.235 42.403
GNG5 guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 subunit. [swissprot;acc:p30670] High confidence 266.864 336.182 69.318
TMEM132A gbp protein isoform a. [refseq;acc:nm_017870] Divided Low confidence 305.399 247.213 1.23537
18 GBE1 1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446] High confidence 185.678 245.247 1.32082
GNG10 guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-10 subunit. [swissprot;acc:p50151] Subtracted 266.865 336.181 69.316
JMJD1A jumonji domain containing 1; zinc finger protein; testis-specific protein a. [refseq;acc:nm_018433] Divided Low confidence 305.303 247.169 1.2352
PRKRAP1 protein kinase, interferon-inducible double stranded rna dependent activator; protein activator of the interferon-induced protein kinase. [refseq;acc:nm_003690] Subtracted 273.188 232.49 40.698
19 no value guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 like subunit. [swissprot;acc:q9y3k8] High confidence 266.865 336.178 69.313
HINT1 histidine triad nucleotide-binding protein 1 (adenosine 5'- monophosphoramidase) (protein kinase c inhibitor 1) (protein kinase c- interacting protein 1) (pkci-1). [swissprot;acc:p49773] Low confidence 188.298 228.509 40.211
PRSS3 trypsin iii precursor (ec 3.4.21.4) (brain trypsinogen) (mesotrypsinogen) (trypsin iv). [swissprot;acc:p35030] Divided 304.548 246.824 1.23387
PYGB glycogen phosphorylase, brain form (ec 2.4.1.1). [swissprot;acc:p11216] High confidence 185.678 245.247 1.32082
20 GNG11 guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-11 subunit. [swissprot;acc:p50152] Subtracted 266.868 336.159 69.291
PRSS1 trypsin i precursor (ec 3.4.21.4) (cationic trypsinogen). [swissprot;acc:p07477] Divided Low confidence 304.359 246.737 1.23354
PYGL glycogen phosphorylase, liver form (ec 2.4.1.1). [swissprot;acc:p06737] High confidence 185.678 245.247 1.32082

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/