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 network_comparison green
Results: HTML CSV LaTeX Showing element 101 to 150 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
Hugo
description
Value Type
red
network_comparison
green
26 GNG10 guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-10 subunit. [swissprot;acc:p50151] Rooted 40.3362 1.66024 24.2954
GNG12 guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-12 subunit. [swissprot;acc:q9ubi6] Measured 1833.01 2.0534 892.67
NEUROD6 neurogenic differentiation factor 6 (neurod6) (my051 protein). [swissprot;acc:q96nk8] Squared 143.692 3.18404 457.521
PANK3 pantothenate kinase 3 (ec 2.7.1.33) (pantothenic acid kinase 3) (hpank3). [swissprot;acc:q9h999] Ranked 58 1.31818 44
27 no value guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 like subunit. [swissprot;acc:q9y3k8] Rooted 40.3364 1.66015 24.2968
GNG4 guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-4 subunit. [swissprot;acc:p50150] Measured 1834.33 2.04922 895.134
NEUROD1 neurogenic differentiation factor 1 (neurod1) (neurod). [swissprot;acc:q13562] Squared 143.692 3.18404 457.521
SLC25A43 mitochondrial solute carrier protein. [refseq;acc:nm_145305] Ranked 58 1.31818 44
28 ATF3 cyclic-amp-dependent transcription factor atf-3 (activating transcription factor 3). [swissprot;acc:p18847] 201.949 1.31416 153.671
GNG11 guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-11 subunit. [swissprot;acc:p50152] Rooted 40.3372 1.65967 24.3043
GNG3 guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-3 subunit. [swissprot;acc:p29798] Measured 1834.36 2.04912 895.194
NEUROD4 neurogenic differentiation factor 4 (neurod4). [swissprot;acc:q9hd90] Squared 143.692 3.18404 457.521
29 CHD5 chromodomain helicase dna binding protein 5. [refseq;acc:nm_015557]
GNG8 guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-8 subunit (gamma-9). [swissprot;acc:q9uk08] Measured 1834.52 2.04858 895.507
PPP1R14A protein phosphatase 1, regulatory (inhibitor) subunit 14a; 17-kda pkc-potentiated inhibitory protein of pp1. [refseq;acc:nm_033256] Rooted 26.0288 1.65937 43.1914
PPP2R2D uncharacterized hematopoietic stem/progenitor cells protein mds026. [sptrembl;acc:q9nz48] Ranked 187.458 1.29991 243.678
30 no value serine/threonine protein phosphatase 2a, 55 kda regulatory subunit b, alpha isoform (pp2a, subunit b, b-alpha isoform) (pp2a, subunit b, b55-alpha isoform) (pp2a, subunit b, pr55-alpha isoform) (pp2a, subunit b, r2-alpha isoform). [swissprot;acc:q00007] 187.457
CDK2AP1 cyclin-dependent kinase 2-associated protein 1 (cdk2-associated protein 1) (putative oral cancer suppressor) (deleted in oral cancer- 1) (doc-1). [swissprot;acc:o14519] Squared 143.692 3.18404 457.521
GNG5 guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 subunit. [swissprot;acc:p30670] Measured 1834.59 2.04837 895.633
MFAP4 microfibril-associated glycoprotein 4 precursor. [swissprot;acc:p55083] Rooted 26.0288 1.65937 43.1914
31 ARRB2 beta-arrestin 2 (arrestin, beta 2). [swissprot;acc:p32121] Squared 9924.76 2.53372 25146.6
GNG10 guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-10 subunit. [swissprot;acc:p50151] Measured 1834.63 2.04827 895.697
PPP1R14D protein phosphatase 1, regulatory subunit 14d; pkc-dependent pp1 inhibitory protein. [refseq;acc:nm_017726] Rooted 26.0288 1.65937 43.1914
PPP2R2B serine/threonine protein phosphatase 2a, 55 kda regulatory subunit b, beta isoform (pp2a, subunit b, b-beta isoform) (pp2a, subunit b, b55- beta isoform) (pp2a, subunit b, pr55-beta isoform) (pp2a, subunit b, r2-beta isoform). [swissprot;acc:q00005] Ranked 187.458 1.2999 243.677
32 no value guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 like subunit. [swissprot;acc:q9y3k8] Measured 1834.73 2.04793 895.893
ARRB1 beta-arrestin 1 (arrestin, beta 1). [swissprot;acc:p49407] Squared 9924.76 2.53372 25146.6
FCN2 ficolin 2 precursor (collagen/fibrinogen domain-containing protein 2) (ficolin-b) (ficolin b) (serum lectin p35) (ebp-37) (hucolin) (l- ficolin). [swissprot;acc:q15485] Rooted 26.0288 1.65937 43.1914
PPP2R2C serine/threonine protein phosphatase 2a, 55 kda regulatory subunit b, gamma isoform (pp2a, subunit b, b-gamma isoform) (pp2a, subunit b, b55-gamma isoform) (pp2a, subunit b, pr55-gamma isoform) (pp2a, subunit b, r2-gamma isoform) (imypno1). [swissprot;acc:q9y2t4] Ranked 187.462 1.29985 243.673
33 no value protein phosphatase 1, regulatory (inhibitor) subunit 14c; serologically defined breast cancer antigen ny-br-81; pkc-potentiated pp1 inhibitory protein. [refseq;acc:nm_030949] Rooted 26.0288 1.65937 43.1914
GNG11 guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-11 subunit. [swissprot;acc:p50152] Measured 1835.3 2.04611 896.972
PPP2R1B serine/threonine protein phosphatase 2a, 65 kda regulatory subunit a, beta isoform (pp2a, subunit a, pr65-beta isoform) (pp2a, subunit a, r1-beta isoform). [swissprot;acc:p30154] Ranked 188.688 1.28647 242.742
SPATA6 spermatogenesis associated 6. [refseq;acc:nm_019073] Squared 9924.76 2.53372 25146.6
34 AMPD2 amp deaminase 2 (ec 3.5.4.6) (amp deaminase isoform l). [swissprot;acc:q01433]
GNA11 guanine nucleotide-binding protein g(y), alpha subunit (alpha-11). [swissprot;acc:p29992] Measured 1836.71 2.02382 907.546
Rooted 40.2812 1.65305 24.3678
PPP2R1A serine/threonine protein phosphatase 2a, 65 kda regulatory subunit a, alpha isoform (pp2a, subunit a, pr65-alpha isoform) (pp2a, subunit a, r1-alpha isoform) (medium tumor antigen-associated 61 kda protein). [swissprot;acc:p30153] Ranked 189.07 1.28235 242.453
35 GNAQ guanine nucleotide-binding protein g(q), alpha subunit. [swissprot;acc:p50148] Measured 1836.71 2.02378 907.564
Rooted 40.2812 1.65304 24.3679
MRPS17 28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5] Squared 106226 1.80879 192141
NFYC nuclear transcription factor y subunit gamma (nf-y protein chain c) (nuclear factor yc) (nf-yc) (ccaat-binding transcription factor subunit c) (cbf-c) (transactivator hsm-1/2). [swissprot;acc:q13952] Ranked 260.532 1.27519 204.309
36 GNAZ guanine nucleotide-binding protein g(z), alpha subunit (g(x) alpha chain) (gz-alpha). [swissprot;acc:p19086] Measured 1836.76 2.02344 907.741
Rooted 40.2805 1.65294 24.369
NFYA ccaat-binding transcription factor subunit b (cbf-b) (nf-y protein chain a) (nf-ya) (caat-box dna binding protein subunit a). [swissprot;acc:p23511] Ranked 260.532 1.27519 204.309
PANK1 pantothenate kinase 1 (ec 2.7.1.33) (pantothenic acid kinase 1) (hpank1) (hpank). [swissprot;acc:q8te04] Squared 106226 1.80879 192141
37 GNAT1 guanine nucleotide-binding protein g(t), alpha-1 subunit (transducin alpha-1 chain). [swissprot;acc:p11488] Measured 1836.76 2.02339 907.763
Rooted 40.2805 1.65293 24.3691
PANK2 pantothenate kinase 2, mitochondrial precursor (ec 2.7.1.33) (pantothenic acid kinase 2) (hpank2). [swissprot;acc:q9bz23] Squared 106226 1.80879 192141
PPP1R14A protein phosphatase 1, regulatory (inhibitor) subunit 14a; 17-kda pkc-potentiated inhibitory protein of pp1. [refseq;acc:nm_033256] Ranked 322 1.27273 253
38 GNAT2 guanine nucleotide-binding protein g(t), alpha-2 subunit (transducin alpha-2 chain). [swissprot;acc:p19087] Measured 1836.76 2.02337 907.774
Rooted 40.2804 1.65292 24.3692

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/