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 Value Type Gene Interaction Map description Filtered green Network Comparison Type network_comparison red
Results: HTML CSV LaTeX Showing element 51 to 100 of 8289 in total
Value Type  : Ranked
Filtered  : 1
Network Comparison Type  : Divided
Rank
Interaction Map
description
green
network_comparison
red
26 High confidence pantothenate kinase 3 (ec 2.7.1.33) (pantothenic acid kinase 3) (hpank3). [swissprot;acc:q9h999] 44 1.31818 58
Low confidence 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] 238.454 1.20085 286.347
27 High confidence mitochondrial solute carrier protein. [refseq;acc:nm_145305] 44 1.31818 58
Low confidence 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] 237.743 1.19792 284.798
28 High confidence cyclic-amp-dependent transcription factor atf-3 (activating transcription factor 3). [swissprot;acc:p18847] 153.671 1.31416 201.949
Low confidence atlastin; guanylate-binding protein 3. [refseq;acc:nm_015915] 170 1.19718 142
29 High confidence uncharacterized hematopoietic stem/progenitor cells protein mds026. [sptrembl;acc:q9nz48] 243.678 1.29991 187.458
Low confidence cyclic-amp-dependent transcription factor atf-3 (activating transcription factor 3). [swissprot;acc:p18847] 170.557 1.19089 203.115
30 High confidence 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] 243.678 1.29991 187.457
Low confidence bcl2-related ovarian killer. [refseq;acc:nm_032515] 223.235 1.18995 265.638
31 High confidence 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] 243.677 1.2999 187.458
Low confidence deoxyribonuclease ii beta isoform 1 precursor; deoxyribonuclease ii beta; endonuclease dlad. [refseq;acc:nm_021233] 48.8186 1.17568 57.395
32 High confidence 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] 243.673 1.29985 187.462
Low confidence protein kinase, interferon-inducible double stranded rna dependent activator; protein activator of the interferon-induced protein kinase. [refseq;acc:nm_003690] 232.49 1.17505 273.188
33 High confidence 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] 242.742 1.28647 188.688
Low confidence 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] 246.125 1.17068 210.241
34 High confidence 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] 242.453 1.28235 189.07
Low confidence putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172] 133.876 1.16197 155.56
35 High confidence 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] 204.309 1.27519 260.532
Low confidence tob2 protein (transducer of erbb-2 2). [swissprot;acc:q14106] 258.59 1.14959 297.273
36 High confidence 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] 204.309 1.27519 260.532
Low confidence tob1 protein (transducer of erbb-2 1). [swissprot;acc:p50616] 258.33 1.14906 296.837
37 High confidence protein phosphatase 1, regulatory (inhibitor) subunit 14a; 17-kda pkc-potentiated inhibitory protein of pp1. [refseq;acc:nm_033256] 253 1.27273 322
Low confidence chromatin accessibility complex protein 1 (chrac-1) (chrac-15) (huchrac15) (dna polymerase epsilon subunit p15). [swissprot;acc:q9nrg0] 217.843 1.14874 250.244
38 High confidence microfibril-associated glycoprotein 4 precursor. [swissprot;acc:p55083] 253 1.27273 322
Low confidence glucosamine-6-phosphate isomerase. [refseq;acc:nm_138335] 282.937 1.14456 247.202
39 High confidence protein phosphatase 1, regulatory subunit 14d; pkc-dependent pp1 inhibitory protein. [refseq;acc:nm_017726] 253 1.27273 322
Low confidence glucosamine-6-phosphate isomerase (ec 3.5.99.6) (glucosamine-6- phosphate deaminase) (gnpda) (glcn6p deaminase) (oscillin). [swissprot;acc:p46926] 282.937 1.14456 247.202
40 High confidence ficolin 2 precursor (collagen/fibrinogen domain-containing protein 2) (ficolin-b) (ficolin b) (serum lectin p35) (ebp-37) (hucolin) (l- ficolin). [swissprot;acc:q15485] 253 1.27273 322
Low confidence 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] 223.538 1.14245 255.382
41 High confidence protein phosphatase 1, regulatory (inhibitor) subunit 14c; serologically defined breast cancer antigen ny-br-81; pkc-potentiated pp1 inhibitory protein. [refseq;acc:nm_030949] 253 1.27273 322
Low confidence ba127l20.1 (novel glutathione-s-transferase). [sptrembl;acc:q9h4y5] 200.55 1.13761 228.147
42 High confidence proto-oncogene protein c-fos (cellular oncogene fos) (g0/g1 switch regulatory protein 7). [swissprot;acc:p01100] 160.957 1.2714 204.641
Low confidence glutathione transferase omega 1 (ec 2.5.1.18) (gsto 1-1). [swissprot;acc:p78417] 200.532 1.13384 227.371
43 High confidence jun dimerization protein. [refseq;acc:nm_130469] 160.957 1.2714 204.641
Low confidence regulator of g-protein signaling 12 (rgs12). [swissprot;acc:o14924] 219.841 1.12703 247.768
44 High confidence fos-related antigen 2. [swissprot;acc:p15408] 161.046 1.2707 204.641
Low confidence protein phosphatase 1, regulatory (inhibitor) subunit 14a; 17-kda pkc-potentiated inhibitory protein of pp1. [refseq;acc:nm_033256] 217.217 1.11751 242.742
45 High confidence protein fosb (g0/g1 switch regulatory protein 3). [swissprot;acc:p53539] 161.051 1.27066 204.641
Low confidence microfibril-associated glycoprotein 4 precursor. [swissprot;acc:p55083] 217.217 1.11751 242.742
46 High confidence fos-related antigen 1 (fra-1). [swissprot;acc:p15407] 161.068 1.27053 204.642
Low confidence protein phosphatase 1, regulatory subunit 14d; pkc-dependent pp1 inhibitory protein. [refseq;acc:nm_017726] 217.217 1.11751 242.742
47 High confidence gbp protein isoform a. [refseq;acc:nm_017870] 256.492 1.26938 325.586
Low confidence ficolin 2 precursor (collagen/fibrinogen domain-containing protein 2) (ficolin-b) (ficolin b) (serum lectin p35) (ebp-37) (hucolin) (l- ficolin). [swissprot;acc:q15485] 217.217 1.11751 242.742
48 High confidence gaba(a) receptor-associated protein; gaba(a)-receptor-associated protein. [refseq;acc:nm_007278] 83.0461 1.26868 65.4586
Low confidence protein phosphatase 1, regulatory (inhibitor) subunit 14c; serologically defined breast cancer antigen ny-br-81; pkc-potentiated pp1 inhibitory protein. [refseq;acc:nm_030949] 217.217 1.11751 242.742
49 High confidence beta-arrestin 2 (arrestin, beta 2). [swissprot;acc:p32121] 105 1.26667 133
Low confidence t-box transcription factor tbx19 (t-box protein 19). [swissprot;acc:o60806] 202.569 1.11289 225.438
50 High confidence beta-arrestin 1 (arrestin, beta 1). [swissprot;acc:p49407] 105 1.26667 133
Low confidence junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2] 260.98 1.11149 234.802

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/