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 description Hugo Network Comparison Type Value Type Interaction Map red Filtered green network_comparison
Results: HTML CSV LaTeX Showing element 73 to 122 of 16578 in total
Value Type  : Ranked
Filtered  : 1
Rank
description
Hugo
Network Comparison Type
Interaction Map
red
green
network_comparison
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
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] HINT1 Low confidence 188.298 228.509 40.211
trypsin iii precursor (ec 3.4.21.4) (brain trypsinogen) (mesotrypsinogen) (trypsin iv). [swissprot;acc:p35030] PRSS3 Divided 304.548 246.824 1.23387
20 glycogen phosphorylase, liver form (ec 2.4.1.1). [swissprot;acc:p06737] PYGL High confidence 185.678 245.247 1.32082
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-11 subunit. [swissprot;acc:p50152] GNG11 Subtracted 266.868 336.159 69.291
tob2 protein (transducer of erbb-2 2). [swissprot;acc:q14106] TOB2 Low confidence 297.273 258.59 38.683
trypsin i precursor (ec 3.4.21.4) (cationic trypsinogen). [swissprot;acc:p07477] PRSS1 Divided 304.359 246.737 1.23354
21 gbp protein isoform a. [refseq;acc:nm_017870] TMEM132A Subtracted High confidence 325.586 256.492 69.094
myosin xv (unconventional myosin-15). [swissprot;acc:q9ukn7] MYO15A Divided 185.678 245.247 1.32082
phosphatidylinositol-glycan biosynthesis, class f protein (pig-f). [swissprot;acc:q07326] PIGF Low confidence 198 163 1.21472
tob1 protein (transducer of erbb-2 1). [swissprot;acc:p50616] TOB1 Subtracted 296.837 258.33 38.507
22 dual specificity mitogen-activated protein kinase kinase 4 (ec 2.7.1.-) (map kinase kinase 4) (jnk activating kinase 1) (c-jun n- terminal kinase kinase 1) (jnkk) (sapk/erk kinase 1) (sek1). [swissprot;acc:p45985] MAP2K4 210.241 246.125 35.884
glycogen phosphorylase, muscle form (ec 2.4.1.1) (myophosphorylase). [swissprot;acc:p11217] PYGM Divided High confidence 185.678 245.247 1.32082
n33 protein. [swissprot;acc:q13454] TUSC3 Low confidence 198 163 1.21472
protein phosphatase 1, regulatory (inhibitor) subunit 14a; 17-kda pkc-potentiated inhibitory protein of pp1. [refseq;acc:nm_033256] PPP1R14A Subtracted High confidence 322 253 69
23 28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5] MRPS17 Divided 58 44 1.31818
glucosamine-6-phosphate isomerase. [refseq;acc:nm_138335] GNPDA2 Subtracted Low confidence 247.202 282.937 35.735
implantation-associated protein. [refseq;acc:nm_032121] no value Divided 198 163 1.21472
microfibril-associated glycoprotein 4 precursor. [swissprot;acc:p55083] MFAP4 Subtracted High confidence 322 253 69
24 glucosamine-6-phosphate isomerase (ec 3.5.99.6) (glucosamine-6- phosphate deaminase) (gnpda) (glcn6p deaminase) (oscillin). [swissprot;acc:p46926] GNPDA1 Low confidence 247.202 282.937 35.735
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] HINT1 Divided 188.298 228.509 1.21355
pantothenate kinase 1 (ec 2.7.1.33) (pantothenic acid kinase 1) (hpank1) (hpank). [swissprot;acc:q8te04] PANK1 High confidence 58 44 1.31818
protein phosphatase 1, regulatory subunit 14d; pkc-dependent pp1 inhibitory protein. [refseq;acc:nm_017726] PPP1R14D Subtracted 322 253 69
25 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 Divided Low confidence 286.396 238.476 1.20094
ficolin 2 precursor (collagen/fibrinogen domain-containing protein 2) (ficolin-b) (ficolin b) (serum lectin p35) (ebp-37) (hucolin) (l- ficolin). [swissprot;acc:q15485] FCN2 Subtracted High confidence 322 253 69
pantothenate kinase 2, mitochondrial precursor (ec 2.7.1.33) (pantothenic acid kinase 2) (hpank2). [swissprot;acc:q9bz23] PANK2 Divided 58 44 1.31818
phosphatidylinositol-glycan biosynthesis, class f protein (pig-f). [swissprot;acc:q07326] PIGF Subtracted Low confidence 198 163 35
26 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 Divided 286.347 238.454 1.20085
n33 protein. [swissprot;acc:q13454] TUSC3 Subtracted 198 163 35
pantothenate kinase 3 (ec 2.7.1.33) (pantothenic acid kinase 3) (hpank3). [swissprot;acc:q9h999] PANK3 Divided High confidence 58 44 1.31818
protein phosphatase 1, regulatory (inhibitor) subunit 14c; serologically defined breast cancer antigen ny-br-81; pkc-potentiated pp1 inhibitory protein. [refseq;acc:nm_030949] no value Subtracted 322 253 69
27 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 Divided Low confidence 284.798 237.743 1.19792
guanine nucleotide-binding protein g(q), alpha subunit. [swissprot;acc:p50148] GNAQ Subtracted High confidence 267.136 336.077 68.941
implantation-associated protein. [refseq;acc:nm_032121] no value Low confidence 198 163 35
mitochondrial solute carrier protein. [refseq;acc:nm_145305] SLC25A43 Divided High confidence 58 44 1.31818
28 atlastin; guanylate-binding protein 3. [refseq;acc:nm_015915] no value Low confidence 142 170 1.19718
cyclic-amp-dependent transcription factor atf-3 (activating transcription factor 3). [swissprot;acc:p18847] ATF3 High confidence 201.949 153.671 1.31416
Subtracted Low confidence 203.115 170.557 32.558
guanine nucleotide-binding protein g(y), alpha subunit (alpha-11). [swissprot;acc:p29992] GNA11 High confidence 267.136 336.077 68.941
29 chromatin accessibility complex protein 1 (chrac-1) (chrac-15) (huchrac15) (dna polymerase epsilon subunit p15). [swissprot;acc:q9nrg0] CHRAC1 Low confidence 250.244 217.843 32.401
cyclic-amp-dependent transcription factor atf-3 (activating transcription factor 3). [swissprot;acc:p18847] ATF3 Divided 203.115 170.557 1.19089
guanine nucleotide-binding protein g(z), alpha subunit (g(x) alpha chain) (gz-alpha). [swissprot;acc:p19086] GNAZ Subtracted High confidence 267.139 336.075 68.936
uncharacterized hematopoietic stem/progenitor cells protein mds026. [sptrembl;acc:q9nz48] PPP2R2D Divided 187.458 243.678 1.29991
30 bcl2-related ovarian killer. [refseq;acc:nm_032515] BOK Low confidence 265.638 223.235 1.18995
guanine nucleotide-binding protein g(t), alpha-2 subunit (transducin alpha-2 chain). [swissprot;acc:p19087] GNAT2 Subtracted High confidence 267.14 336.075 68.935
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] no value Divided 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] SON Subtracted Low confidence 255.382 223.538 31.844
31 atlastin; guanylate-binding protein 3. [refseq;acc:nm_015915] no value 142 170 28
deoxyribonuclease ii beta isoform 1 precursor; deoxyribonuclease ii beta; endonuclease dlad. [refseq;acc:nm_021233] DNASE2B Divided 57.395 48.8186 1.17568

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/