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 Hugo Value Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 1408 to 1457 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
Hugo
Value Type
red
green
network_comparison
176 proprotein convertase subtilisin/kexin type 5 precursor (ec 3.4.21.-) (proprotein convertase pc5) (subtilisin/kexin-like protease pc5) (convertase pc5) (pc6) (hpc6). [swissprot;acc:q92824] Subtracted PCSK5 Squared 71576.8 56326.7 15250.1
177 beta-arrestin 2 (arrestin, beta 2). [swissprot;acc:p32121] ARRB2 9924.76 25146.6 15221.8
dj820b18.1 (similar to nuclear cap binding protein) (fragment). [sptrembl;acc:q8wwk2] Divided NCBP2L Ranked 229.406 196.695 1.1663
lag1 longevity assurance homolog 2 isoform 1; l3 pigment; tumor metastasis-suppressor. [refseq;acc:nm_022075] Subtracted LASS2 Measured 4110.14 5694.99 1584.85
max dimerization protein 3; likely ortholog of mouse max dimerization protein 3. [refseq;acc:nm_031300] Divided RAB24 4457.06 5773.63 1.29539
mitochondrial solute carrier protein. [refseq;acc:nm_145305] SLC25A43 Rooted 145.551 168.796 1.1597
presenilin 1 (ps-1) (s182 protein). [swissprot;acc:p49768] Subtracted PSEN1 37.3005 48.4141 11.1136
septin 1 (larp) (serologically defined breast cancer antigen ny-br- 24). [swissprot;acc:q8wyj6] Divided SEPT1 Squared 78383 108483 1.38401
transcriptional co-repressor sin3a; transcriptional regulator, sin3a (yeast). [refseq;acc:nm_015477] Subtracted SIN3A Ranked 241.07 267.88 26.81
178 beta-arrestin 1 (arrestin, beta 1). [swissprot;acc:p49407] ARRB1 Squared 9924.76 25146.6 15221.8
carboxypeptidase b precursor. [refseq;acc:nm_020361] Divided CPA6 25326.4 18354.1 1.37988
cullin homolog 1 (cul-1). [swissprot;acc:q13616] Subtracted CUL1 Rooted 37.3005 48.4141 11.1136
density-regulated protein (drp) (drp1 protein) (smooth muscle cell associated protein-3) (smap-3). [swissprot;acc:o43583] DENR Ranked 241.07 267.88 26.81
formin binding protein 3; fas-ligand associated factor 1; huntingtin-interacting protein a; ny-ren-6 antigen. [refseq;acc:nm_017892] Divided no value 226.887 194.72 1.1652
myosin vb (myosin 5b) (fragment). [swissprot;acc:q9ulv0] MYO5B Measured 21591.5 27904.5 1.29238
stem cell growth factor; lymphocyte secreted c-type lectin; lymphocyte secreted c-type lectin. [refseq;acc:nm_002975] Subtracted CLEC11A 10908.6 12491.8 1583.2
transcription factor dp-2 (e2f dimerization partner 2). [swissprot;acc:q14188] Divided TFDP2 Rooted 45.7414 52.932 1.1572
179 20 kda nuclear cap binding protein (ncbp 20 kda subunit) (cbp20) (ncbp interacting protein 1) (nip1). [swissprot;acc:p52298] Subtracted NCBP2 Measured 4266.04 5843.51 1577.47
huntingtin interacting protein c. [refseq;acc:nm_012272] PRPF40B Rooted 55.0737 66.0298 10.9561
huntingtin-interacting protein hypa/fbp11 (fragment). [sptrembl;acc:o75404] Divided no value Ranked 226.884 194.79 1.16476
mast cell carboxypeptidase a precursor (ec 3.4.17.1) (mc-cpa) (carboxypeptidase a3). [swissprot;acc:p15088] CPA3 Squared 25326.3 18354.1 1.37987
myosin vc (myosin 5c). [swissprot;acc:q9nqx4] MYO5C Measured 21591.5 27904.5 1.29238
palmitoyl-protein thioesterase 2 precursor (ec 3.1.2.22) (palmitoyl- protein hydrolase 2) (ppt-2) (g14). [swissprot;acc:q9umr5] EGFL8 Rooted 50.272 43.4634 1.15665
phenylalanine-4-hydroxylase (ec 1.14.16.1) (pah) (phe-4- monooxygenase). [swissprot;acc:p00439] Subtracted PAH Ranked 227.357 254.15 26.793
spermatogenesis associated 6. [refseq;acc:nm_019073] SPATA6 Squared 9924.76 25146.6 15221.8
180 amp deaminase 2 (ec 3.5.4.6) (amp deaminase isoform l). [swissprot;acc:q01433] AMPD2
c-type lectin superfamily member 1 precursor (cartilage-derived c-type lectin). [swissprot;acc:o75596] CLEC3A Measured 10872.4 12447 1574.6
egf-like-domain, multiple 7; neu1 protein. [refseq;acc:nm_016215] Divided EGFL7 Rooted 50.2801 43.4779 1.15645
metalloprotease 1; metalloprotease 1 (pitrilysin family). [refseq;acc:nm_014889] Subtracted PITRM1 88.4361 77.5112 10.9249
myosin va (myosin 5a) (dilute myosin heavy chain, non-muscle) (myosin heavy chain 12) (myoxin). [swissprot;acc:q9y4i1] Divided no value Measured 21591.5 27904.5 1.29238
plasma carboxypeptidase b2 isoform a preproprotein; carboxypeptidase u; thrombin-activatable fibrinolysis inhibitor; carboxypeptidase b-like protein; thrombin-activable fibrinolysis inhibitor. [refseq;acc:nm_001872] CPB2 Squared 25326.2 18354.1 1.37987
pp3111 protein. [refseq;acc:nm_022156] Subtracted DUS1L Ranked 227.357 254.15 26.793
tar dna-binding protein-43 (tdp-43). [swissprot;acc:q13148] Divided TARDBP 256.228 298.438 1.16474
181 b9 protein; likely ortholog of mouse endothelial precursor protein b9. [refseq;acc:nm_015681] B9D1 229.818 267.265 1.16294
beta-1,4 mannosyltransferase. [refseq;acc:nm_019109] Subtracted ALG1 Rooted 88.4266 77.5047 10.9219
crk-associated substrate (p130cas) (breast cancer anti-estrogen resistance 1 protein). [swissprot;acc:p56945] Divided BCAR1 57.4432 66.3307 1.15472
eukaryotic translation initiation factor 4 gamma, 3. [refseq;acc:nm_003760] EIF4G3 Measured 4068.56 5252.6 1.29102
hira-interacting protein 5 (cgi-33). [swissprot;acc:q9ums0] NFU1 Squared 55630.4 76083.7 1.36766
musashi 2 isoform a. [refseq;acc:nm_138962] Subtracted MSI2 Measured 4241.57 5810.79 1569.22
syntaxin 18. [swissprot;acc:q9p2w9] STX18 Ranked 227.357 254.15 26.793
transcription factor iib. [refseq;acc:nm_013242] C16orf80 Squared 64739.9 50300.6 14439.3
182 chromosome 3p21.1 gene sequence. [refseq;acc:nm_013286] RBM15B Rooted 47.6504 36.9304 10.72
deoxyuridine 5'-triphosphate nucleotidohydrolase, mitochondrial precursor (ec 3.6.1.23) (dutpase) (dutp pyrophosphatase). [swissprot;acc:p33316] Divided DUT Squared 61733.5 45224.1 1.36506
histone acetyltransferase type b catalytic subunit (ec 2.3.1.48). [swissprot;acc:o14929] HAT1 Ranked 277.546 240.461 1.15422
musashi 1. [refseq;acc:nm_002442] Subtracted MSI1 Measured 4241.57 5810.79 1569.22
rd protein. [swissprot;acc:p18615] no value Ranked 227.357 254.15 26.793
rna-binding protein. [refseq;acc:nm_019027] Divided Measured 4069.83 5252.17 1.29051
splicing factor, arginine/serine-rich 8 (suppressor of white apricot protein homolog). [swissprot;acc:q12872] Subtracted SFRS8 Squared 64739.9 50300.6 14439.3
t-complex protein 1, delta subunit (tcp-1-delta) (cct-delta) (stimulator of tar rna binding). [swissprot;acc:p50991] Divided CCT4 Rooted 57.45 66.332 1.1546
183 20 kda nuclear cap binding protein (ncbp 20 kda subunit) (cbp20) (ncbp interacting protein 1) (nip1). [swissprot;acc:p52298] NCBP2 Ranked 228.306 198.011 1.153

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/