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 - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.


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 Hugo description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 223 to 272 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
Hugo
description
Value Type
Network Comparison Type
red
green
network_comparison
28 NDN necdin. [swissprot;acc:q99608] Measured Subtracted 23693.7 18263 5430.7
NEUROD4 neurogenic differentiation factor 4 (neurod4). [swissprot;acc:q9hd90] Squared Divided 143.692 457.521 3.18404
29 CHD5 chromodomain helicase dna binding protein 5. [refseq;acc:nm_015557]
GNAZ guanine nucleotide-binding protein g(z), alpha subunit (g(x) alpha chain) (gz-alpha). [swissprot;acc:p19086] Ranked Subtracted 267.139 336.075 68.936
GNG8 guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-8 subunit (gamma-9). [swissprot;acc:q9uk08] Measured Divided 1834.52 895.507 2.04858
MAGED1 melanoma-associated antigen d1 (mage-d1 antigen) (neurotrophin receptor-interacting mage homolog) (pro2292). [swissprot;acc:q9y5v3] Subtracted 23693.7 18263 5430.7
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] Squared 219048 129762 89286
PPP1R14A protein phosphatase 1, regulatory (inhibitor) subunit 14a; 17-kda pkc-potentiated inhibitory protein of pp1. [refseq;acc:nm_033256] Rooted Divided 26.0288 43.1914 1.65937
PPP2R2D uncharacterized hematopoietic stem/progenitor cells protein mds026. [sptrembl;acc:q9nz48] Ranked 187.458 243.678 1.29991
UBAC1 putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172] Rooted Subtracted 210.928 192.165 18.763
30 no value 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] Ranked Divided 187.457 243.678 1.29991
ATF3 cyclic-amp-dependent transcription factor atf-3 (activating transcription factor 3). [swissprot;acc:p18847] Rooted Subtracted 60.8022 79.5099 18.7077
CDK2AP1 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] Squared Divided 143.692 457.521 3.18404
GNAT2 guanine nucleotide-binding protein g(t), alpha-2 subunit (transducin alpha-2 chain). [swissprot;acc:p19087] Ranked Subtracted 267.14 336.075 68.935
GNG5 guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 subunit. [swissprot;acc:p30670] Measured Divided 1834.59 895.633 2.04837
MAGEF1 melanoma-associated antigen f1 (mage-f1 antigen). [swissprot;acc:q9hay2] Subtracted 23693.7 18263 5430.7
MFAP4 microfibril-associated glycoprotein 4 precursor. [swissprot;acc:p55083] Rooted Divided 26.0288 43.1914 1.65937
TRO trophinin. [swissprot;acc:q12816] Squared Subtracted 219048 129762 89286
31 ARRB2 beta-arrestin 2 (arrestin, beta 2). [swissprot;acc:p32121] Divided 9924.76 25146.6 2.53372
GNAT1 guanine nucleotide-binding protein g(t), alpha-1 subunit (transducin alpha-1 chain). [swissprot;acc:p11488] Ranked Subtracted 267.14 336.075 68.935
GNG10 guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-10 subunit. [swissprot;acc:p50151] Measured Divided 1834.63 895.697 2.04827
MAGEB6B melanoma antigen, family b, 6. [refseq;acc:nm_173523] Subtracted 23693.7 18263 5430.7
MRPS17 28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5] Squared 106226 192141 85915
PPP1R14D protein phosphatase 1, regulatory subunit 14d; pkc-dependent pp1 inhibitory protein. [refseq;acc:nm_017726] Rooted Divided 26.0288 43.1914 1.65937
PPP2R2B 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
UFC1 protein cgi-126 (protein hspc155). [swissprot;acc:q9y3c8] Rooted Subtracted 40.0958 58.7986 18.7028
32 no value guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 like subunit. [swissprot;acc:q9y3k8] Measured Divided 1834.73 895.893 2.04793
melanoma-associated antigen 4 (mage-4 antigen) (mage-x2) (mage-41). [swissprot;acc:p43358] Subtracted 23693.7 18263 5430.7
ARRB1 beta-arrestin 1 (arrestin, beta 1). [swissprot;acc:p49407] Squared Divided 9924.76 25146.6 2.53372
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 43.1914 1.65937
GNAI2 guanine nucleotide-binding protein g(i), alpha-2 subunit (adenylate cyclase-inhibiting g alpha protein). [swissprot;acc:p04899] Ranked Subtracted 267.142 336.074 68.932
PANK1 pantothenate kinase 1 (ec 2.7.1.33) (pantothenic acid kinase 1) (hpank1) (hpank). [swissprot;acc:q8te04] Squared 106226 192141 85915
PPP2R2C 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] Ranked Divided 187.462 243.673 1.29985
TMEM132A gbp protein isoform a. [refseq;acc:nm_017870] Rooted Subtracted 23.9771 42.4773 18.5002
33 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 26.0288 43.1914 1.65937
GNAI1 guanine nucleotide-binding protein g(i), alpha-1 subunit (adenylate cyclase-inhibiting g alpha protein). [swissprot;acc:p04898] Ranked Subtracted 267.144 336.073 68.929
GNG11 guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-11 subunit. [swissprot;acc:p50152] Measured Divided 1835.3 896.972 2.04611
MAGEA9 melanoma-associated antigen 9 (mage-9 antigen). [swissprot;acc:p43362] Subtracted 23693.7 18263 5430.7
PANK2 pantothenate kinase 2, mitochondrial precursor (ec 2.7.1.33) (pantothenic acid kinase 2) (hpank2). [swissprot;acc:q9bz23] Squared 106226 192141 85915
PPP2R1B 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] Ranked Divided 188.688 242.742 1.28647
PRKRAP1 protein kinase, interferon-inducible double stranded rna dependent activator; protein activator of the interferon-induced protein kinase. [refseq;acc:nm_003690] Rooted Subtracted 25.6987 43.561 17.8623
SPATA6 spermatogenesis associated 6. [refseq;acc:nm_019073] Squared Divided 9924.76 25146.6 2.53372
34 no value gaba-a receptor-associated protein. [sptrembl;acc:q9by60] Rooted Subtracted 140.508 122.878 17.63
AMPD2 amp deaminase 2 (ec 3.5.4.6) (amp deaminase isoform l). [swissprot;acc:q01433] Squared Divided 9924.76 25146.6 2.53372
GNA11 guanine nucleotide-binding protein g(y), alpha subunit (alpha-11). [swissprot;acc:p29992] Measured 1836.71 907.546 2.02382
Rooted 40.2812 24.3678 1.65305
GNAI3 guanine nucleotide-binding protein g(k), alpha subunit (g(i) alpha-3). [swissprot;acc:p08754] Ranked Subtracted 267.144 336.073 68.929
MAGEA8 melanoma-associated antigen 8 (mage-8 antigen). [swissprot;acc:p43361] Measured 23693.7 18263 5430.7
PANK3 pantothenate kinase 3 (ec 2.7.1.33) (pantothenic acid kinase 3) (hpank3). [swissprot;acc:q9h999] Squared 106226 192141 85915
PPP2R1A 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] Ranked Divided 189.07 242.453 1.28235

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/