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 275 to 324 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
Hugo
description
Network Comparison Type
Value Type
red
network_comparison
green
35 GNAQ guanine nucleotide-binding protein g(q), alpha subunit. [swissprot;acc:p50148] Divided Rooted 40.2812 1.65304 24.3679
GNB5 guanine nucleotide-binding protein beta subunit 5 (transducin beta chain 5). [swissprot;acc:o14775] Subtracted Ranked 267.636 67.723 335.359
MAGEC1 melanoma-associated antigen c1 (mage-c1 antigen) (cancer-testis antigen ct7). [swissprot;acc:o60732] Measured 23693.7 5430.7 18263
MRPS17 28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5] Divided 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
SLC25A43 mitochondrial solute carrier protein. [refseq;acc:nm_145305] Subtracted Squared 106226 85915 192141
36 CPSF4 cleavage and polyadenylation specific factor 4, 30kd subunit; cleavage-polyadenylation specificity factor, 30kd; no arches-like (zebrafish) zinc finger protein; cleavage-polyadenylation specificity factor. [refseq;acc:nm_006693] 227160 81081 146079
GNAZ guanine nucleotide-binding protein g(z), alpha subunit (g(x) alpha chain) (gz-alpha). [swissprot;acc:p19086] Divided Measured 1836.76 2.02344 907.741
Rooted 40.2805 1.65294 24.369
MAGEA4 melanoma-associated antigen 12 (mage-12 antigen) (mage12f). [swissprot;acc:p43365] Subtracted Measured 23693.7 5430.7 18263
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] Divided 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
PPP1R14A protein phosphatase 1, regulatory (inhibitor) subunit 14a; 17-kda pkc-potentiated inhibitory protein of pp1. [refseq;acc:nm_033256] Subtracted Rooted 26.0288 17.1626 43.1914
PRKRAP1 protein kinase, interferon-inducible double stranded rna dependent activator; protein activator of the interferon-induced protein kinase. [refseq;acc:nm_003690] Ranked 320.927 66.493 254.434
37 no value melanoma-associated antigen 1 (mage-1 antigen) (antigen mz2-e). [swissprot;acc:p43355] Measured 23693.7 5430.7 18263
GNAT1 guanine nucleotide-binding protein g(t), alpha-1 subunit (transducin alpha-1 chain). [swissprot;acc:p11488] Divided 1836.76 2.02339 907.763
Rooted 40.2805 1.65293 24.3691
GNB1 guanine nucleotide-binding protein g(i)/g(s)/g(t) beta subunit 1 (transducin beta chain 1). [swissprot;acc:p04901] Subtracted Ranked 266.716 66.449 333.165
KIAA1012 trs85 homolog. [swissprot;acc:q9y2l5] Squared 227160 81081 146079
MFAP4 microfibril-associated glycoprotein 4 precursor. [swissprot;acc:p55083] Rooted 26.0288 17.1626 43.1914
PANK2 pantothenate kinase 2, mitochondrial precursor (ec 2.7.1.33) (pantothenic acid kinase 2) (hpank2). [swissprot;acc:q9bz23] Divided 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
GNB4 guanine nucleotide-binding protein beta subunit 4 (transducin beta chain 4). [swissprot;acc:q9hav0] Subtracted Ranked 266.933 66.348 333.281
MAGEA10 melanoma-associated antigen 10 (mage-10 antigen). [swissprot;acc:p43363] Measured 23693.7 5430.7 18263
MFAP4 microfibril-associated glycoprotein 4 precursor. [swissprot;acc:p55083] Divided Ranked 322 1.27273 253
PANK3 pantothenate kinase 3 (ec 2.7.1.33) (pantothenic acid kinase 3) (hpank3). [swissprot;acc:q9h999] Squared 106226 1.80879 192141
PPP1R14D protein phosphatase 1, regulatory subunit 14d; pkc-dependent pp1 inhibitory protein. [refseq;acc:nm_017726] Subtracted Rooted 26.0288 17.1626 43.1914
WDR33 wd-repeat protein wdc146. [swissprot;acc:q9c0j8] Squared 226186 80618 145568
39 CPSF1 cleavage and polyadenylation specificity factor, 160 kda subunit (cpsf 160 kda subunit). [swissprot;acc:q10570]
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 17.1626 43.1914
GNAI2 guanine nucleotide-binding protein g(i), alpha-2 subunit (adenylate cyclase-inhibiting g alpha protein). [swissprot;acc:p04899] Divided Measured 1836.8 2.02312 907.903
Rooted 40.28 1.65285 24.37
GNB3 guanine nucleotide-binding protein g(i)/g(s)/g(t) beta subunit 3 (transducin beta chain 3). [swissprot;acc:p16520] Subtracted Ranked 268.565 65.918 334.483
MAGEB4 melanoma-associated antigen b1 (mage-b1 antigen) (mage-xp antigen) (dss-ahc critical interval mage superfamily 10) (dam10). [swissprot;acc:p43366] Measured 23693.7 5430.7 18263
PPP1R14D protein phosphatase 1, regulatory subunit 14d; pkc-dependent pp1 inhibitory protein. [refseq;acc:nm_017726] Divided Ranked 322 1.27273 253
SLC25A43 mitochondrial solute carrier protein. [refseq;acc:nm_145305] Squared 106226 1.80879 192141
40 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] Subtracted Rooted 26.0288 17.1626 43.1914
ATG4A cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936] Divided Squared 144940 1.78564 81169.7
CPSF2 cleavage and polyadenylation specificity factor, 100 kda subunit (cpsf 100 kda subunit) (fragment). [swissprot;acc:q9p2i0] Subtracted 222655 79071 143584
DTX2 deltex 2. [refseq;acc:nm_020892] Ranked 333.144 65.751 267.393
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] Divided 322 1.27273 253
GNAI1 guanine nucleotide-binding protein g(i), alpha-1 subunit (adenylate cyclase-inhibiting g alpha protein). [swissprot;acc:p04898] Measured 1836.81 2.02297 907.978
Rooted 40.2797 1.65281 24.3705
MAGED2 melanoma-associated antigen d2 (mage-d2 antigen) (breast cancer associated gene 1 protein) (bcg-1) (11b6) (hepatocellular carcinoma associated protein jcl-1). [swissprot;acc:q9unf1] Subtracted Measured 23693.7 5430.7 18263
41 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] Divided Ranked 322 1.27273 253
DTX1 deltex homolog 1; hdx-1. [refseq;acc:nm_004416] Subtracted 332.925 65.651 267.274
FIP1L1 fip1-like 1; rearranged in hypereosinophilia. [refseq;acc:nm_030917] Squared 214143 75806 138337
FOS proto-oncogene protein c-fos (cellular oncogene fos) (g0/g1 switch regulatory protein 7). [swissprot;acc:p01100] Rooted 60.8365 16.8868 77.7233

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/