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.


Navigation/Query Panel:
Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].
Rank Gene description Value Type Network Comparison Type Interaction Map red Filtered network_comparison green
Results: HTML CSV LaTeX Showing element 51 to 100 of 16578 in total
Value Type  : Ranked
Filtered  : 1
Rank
description
Network Comparison Type
Interaction Map
red
network_comparison
green
13 protein cgi-126 (protein hspc155). [swissprot;acc:q9y3c8] Divided High confidence 288.754 1.3585 212.554
Subtracted Low confidence 255.046 52.684 202.362
14 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] 286.396 47.92 238.476
cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936] Divided High confidence 56.6768 1.32952 75.3531
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-4 subunit. [swissprot;acc:p50150] Subtracted 266.863 69.328 336.191
vitelliform macular dystrophy 2-like protein 1. [refseq;acc:nm_017682] Divided Low confidence 37.9984 1.30207 29.1831
15 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] Subtracted 286.347 47.893 238.454
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-3 subunit. [swissprot;acc:p29798] High confidence 266.863 69.327 336.19
microtubule-associated proteins 1a/1b light chain 3b (map1a/map1b lc3 b) (map1a/1b light chain 3 b). [swissprot;acc:q9gzq8] Divided 56.7244 1.32914 75.3948
protein cgi-126 (protein hspc155). [swissprot;acc:q9y3c8] Low confidence 255.046 1.26035 202.362
16 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 47.055 237.743
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-8 subunit (gamma-9). [swissprot;acc:q9uk08] High confidence 266.864 69.32 336.184
microtubule-associated proteins 1a/1b light chain 3a (map1a/map1b lc3 a) (map1a/1b light chain 3 a). [swissprot;acc:q9h492] Divided 56.7252 1.32913 75.3954
thyroid receptor interacting protein 8 (trip-8) (fragment). [swissprot;acc:q15652] Low confidence 305.472 1.2355 247.246
17 bcl2-related ovarian killer. [refseq;acc:nm_032515] Subtracted 265.638 42.403 223.235
cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326] Divided High confidence 56.7841 1.32866 75.447
gbp protein isoform a. [refseq;acc:nm_017870] Low confidence 305.399 1.23537 247.213
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 subunit. [swissprot;acc:p30670] Subtracted High confidence 266.864 69.318 336.182
18 1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446] Divided 185.678 1.32082 245.247
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-10 subunit. [swissprot;acc:p50151] Subtracted 266.865 69.316 336.181
jumonji domain containing 1; zinc finger protein; testis-specific protein a. [refseq;acc:nm_018433] Divided Low confidence 305.303 1.2352 247.169
protein kinase, interferon-inducible double stranded rna dependent activator; protein activator of the interferon-induced protein kinase. [refseq;acc:nm_003690] Subtracted 273.188 40.698 232.49
19 glycogen phosphorylase, brain form (ec 2.4.1.1). [swissprot;acc:p11216] Divided High confidence 185.678 1.32082 245.247
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 like subunit. [swissprot;acc:q9y3k8] Subtracted 266.865 69.313 336.178
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 40.211 228.509
trypsin iii precursor (ec 3.4.21.4) (brain trypsinogen) (mesotrypsinogen) (trypsin iv). [swissprot;acc:p35030] Divided 304.548 1.23387 246.824
20 glycogen phosphorylase, liver form (ec 2.4.1.1). [swissprot;acc:p06737] High confidence 185.678 1.32082 245.247
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-11 subunit. [swissprot;acc:p50152] Subtracted 266.868 69.291 336.159
tob2 protein (transducer of erbb-2 2). [swissprot;acc:q14106] Low confidence 297.273 38.683 258.59
trypsin i precursor (ec 3.4.21.4) (cationic trypsinogen). [swissprot;acc:p07477] Divided 304.359 1.23354 246.737
21 gbp protein isoform a. [refseq;acc:nm_017870] Subtracted High confidence 325.586 69.094 256.492
myosin xv (unconventional myosin-15). [swissprot;acc:q9ukn7] Divided 185.678 1.32082 245.247
phosphatidylinositol-glycan biosynthesis, class f protein (pig-f). [swissprot;acc:q07326] Low confidence 198 1.21472 163
tob1 protein (transducer of erbb-2 1). [swissprot;acc:p50616] Subtracted 296.837 38.507 258.33
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] 210.241 35.884 246.125
glycogen phosphorylase, muscle form (ec 2.4.1.1) (myophosphorylase). [swissprot;acc:p11217] Divided High confidence 185.678 1.32082 245.247
n33 protein. [swissprot;acc:q13454] Low confidence 198 1.21472 163
protein phosphatase 1, regulatory (inhibitor) subunit 14a; 17-kda pkc-potentiated inhibitory protein of pp1. [refseq;acc:nm_033256] Subtracted High confidence 322 69 253
23 28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5] Divided 58 1.31818 44
glucosamine-6-phosphate isomerase. [refseq;acc:nm_138335] Subtracted Low confidence 247.202 35.735 282.937
implantation-associated protein. [refseq;acc:nm_032121] Divided 198 1.21472 163
microfibril-associated glycoprotein 4 precursor. [swissprot;acc:p55083] Subtracted High confidence 322 69 253
24 glucosamine-6-phosphate isomerase (ec 3.5.99.6) (glucosamine-6- phosphate deaminase) (gnpda) (glcn6p deaminase) (oscillin). [swissprot;acc:p46926] Low confidence 247.202 35.735 282.937
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] Divided 188.298 1.21355 228.509
pantothenate kinase 1 (ec 2.7.1.33) (pantothenic acid kinase 1) (hpank1) (hpank). [swissprot;acc:q8te04] High confidence 58 1.31818 44
protein phosphatase 1, regulatory subunit 14d; pkc-dependent pp1 inhibitory protein. [refseq;acc:nm_017726] Subtracted 322 69 253
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] Divided Low confidence 286.396 1.20094 238.476
ficolin 2 precursor (collagen/fibrinogen domain-containing protein 2) (ficolin-b) (ficolin b) (serum lectin p35) (ebp-37) (hucolin) (l- ficolin). [swissprot;acc:q15485] Subtracted High confidence 322 69 253
pantothenate kinase 2, mitochondrial precursor (ec 2.7.1.33) (pantothenic acid kinase 2) (hpank2). [swissprot;acc:q9bz23] Divided 58 1.31818 44
phosphatidylinositol-glycan biosynthesis, class f protein (pig-f). [swissprot;acc:q07326] Subtracted Low confidence 198 35 163

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/