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 Network Comparison Type Interaction Map Filtered Value Type red green network_comparison
Results: HTML CSV LaTeX Showing element 451 to 500 of 66312 in total
Filtered  : 1
Rank
description
Network Comparison Type
Interaction Map
Value Type
red
green
network_comparison
29 cyclic-amp-dependent transcription factor atf-3 (activating transcription factor 3). [swissprot;acc:p18847] Divided Low confidence Ranked 203.115 170.557 1.19089
cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418] Subtracted Squared 92930.5 71802.4 21128.1
cytoplasmic polyadenylation element binding protein 3. [refseq;acc:nm_014912] Divided Rooted 48.8531 56.7071 1.16077
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-8 subunit (gamma-9). [swissprot;acc:q9uk08] High confidence Measured 1834.52 895.507 2.04858
guanine nucleotide-binding protein g(z), alpha subunit (g(x) alpha chain) (gz-alpha). [swissprot;acc:p19086] Subtracted Ranked 267.139 336.075 68.936
hepatocellular carcinoma-associated protein hca3. [refseq;acc:nm_138703] Divided Low confidence Squared 82347.8 61881.5 1.33073
melanoma-associated antigen d1 (mage-d1 antigen) (neurotrophin receptor-interacting mage homolog) (pro2292). [swissprot;acc:q9y5v3] Subtracted High confidence Measured 23693.7 18263 5430.7
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] Squared 219048 129762 89286
protein phosphatase 1, regulatory (inhibitor) subunit 14a; 17-kda pkc-potentiated inhibitory protein of pp1. [refseq;acc:nm_033256] Divided Rooted 26.0288 43.1914 1.65937
putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172] Subtracted 210.928 192.165 18.763
retinoblastoma-associated factor 600. [refseq;acc:nm_020765] Low confidence 76.5734 88.6244 12.051
septin 10 isoform 1. [refseq;acc:nm_144710] Measured 13081.2 14872.6 1791.4
tob1 protein (transducer of erbb-2 1). [swissprot;acc:p50616] Divided 3121.28 3739.84 1.19818
uncharacterized hematopoietic stem/progenitor cells protein mds026. [sptrembl;acc:q9nz48] High confidence Ranked 187.458 243.678 1.29991
30 bcl2-related ovarian killer. [refseq;acc:nm_032515] Low confidence 265.638 223.235 1.18995
bestrophin (vitelliform macular dystrophy protein) (tu15b). [swissprot;acc:o76090] Measured 36474.3 43509.4 1.19288
cyclic-amp-dependent transcription factor atf-3 (activating transcription factor 3). [swissprot;acc:p18847] Subtracted High confidence Rooted 60.8022 79.5099 18.7077
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] Divided Squared 143.692 457.521 3.18404
cytoplasmic polyadenylation element binding protein 4. [refseq;acc:nm_030627] Low confidence Rooted 48.8781 56.7253 1.16055
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 subunit. [swissprot;acc:p30670] High confidence Measured 1834.59 895.633 2.04837
guanine nucleotide-binding protein g(t), alpha-2 subunit (transducin alpha-2 chain). [swissprot;acc:p19087] Subtracted Ranked 267.14 336.075 68.935
mannosyl-oligosaccharide 1,2-alpha-mannosidase ib (ec 3.2.1.113) (processing alpha-1,2-mannosidase ib) (alpha-1,2-mannosidase ib) (mannosidase alpha class 1a member 2). [swissprot;acc:o60476] Low confidence Squared 92930 71802.1 21127.9
melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [swissprot;acc:p43357] Divided 82347.8 61881.5 1.33073
melanoma-associated antigen f1 (mage-f1 antigen). [swissprot;acc:q9hay2] Subtracted High confidence Measured 23693.7 18263 5430.7
microfibril-associated glycoprotein 4 precursor. [swissprot;acc:p55083] Divided Rooted 26.0288 43.1914 1.65937
phosphatidylinositol-glycan biosynthesis, class f protein (pig-f). [swissprot;acc:q07326] Subtracted Low confidence Measured 3278 5058.5 1780.5
protein kinase, interferon-inducible double stranded rna dependent activator; protein activator of the interferon-induced protein kinase. [refseq;acc:nm_003690] Rooted 44.4168 55.937 11.5202
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] Divided High confidence Ranked 187.457 243.678 1.29991
son protein (son3) (negative regulatory element-binding protein) (nre- binding protein) (dbp-5) (bax antagonist selected in saccharomyces 1) (bass1) (protein c21orf50). [swissprot;acc:p18583] Subtracted Low confidence 255.382 223.538 31.844
trophinin. [swissprot;acc:q12816] High confidence Squared 219048 129762 89286
31 28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5] Divided Low confidence Rooted 145.551 168.796 1.1597
Subtracted High confidence Squared 106226 192141 85915
atlastin; guanylate-binding protein 3. [refseq;acc:nm_015915] Low confidence Ranked 142 170 28
beta-arrestin 2 (arrestin, beta 2). [swissprot;acc:p32121] Divided High confidence Squared 9924.76 25146.6 2.53372
cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739] Subtracted Low confidence 92920.4 71796.4 21124
deoxyribonuclease ii beta isoform 1 precursor; deoxyribonuclease ii beta; endonuclease dlad. [refseq;acc:nm_021233] Divided Ranked 57.395 48.8186 1.17568
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-10 subunit. [swissprot;acc:p50151] High confidence Measured 1834.63 895.697 2.04827
guanine nucleotide-binding protein g(t), alpha-1 subunit (transducin alpha-1 chain). [swissprot;acc:p11488] Subtracted Ranked 267.14 336.075 68.935
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 Rooted 67.7094 56.875 10.8344
melanoma antigen, family b, 6. [refseq;acc:nm_173523] High confidence Measured 23693.7 18263 5430.7
melanoma-associated antigen 11 (mage-11 antigen). [swissprot;acc:p43364] Divided Low confidence Squared 82347.8 61881.5 1.33073
n33 protein. [swissprot;acc:q13454] Subtracted Measured 3278 5058.5 1780.5
protein cgi-126 (protein hspc155). [swissprot;acc:q9y3c8] High confidence Rooted 40.0958 58.7986 18.7028
protein phosphatase 1, regulatory subunit 14d; pkc-dependent pp1 inhibitory protein. [refseq;acc:nm_017726] Divided 26.0288 43.1914 1.65937
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 187.458 243.677 1.2999
vitelliform macular dystrophy 2-like protein 2. [refseq;acc:nm_153274] Low confidence Measured 36469.3 43503.3 1.19287
32 beta-arrestin 1 (arrestin, beta 1). [swissprot;acc:p49407] High confidence Squared 9924.76 25146.6 2.53372
cytohesin 4. [swissprot;acc:q9uia0] Subtracted Low confidence 92262.9 71400.2 20862.7
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 High confidence Rooted 26.0288 43.1914 1.65937
gbp protein isoform a. [refseq;acc:nm_017870] Subtracted 23.9771 42.4773 18.5002

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/