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 Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 680 to 729 of 8289 in total
Value Type  : Ranked
Network Comparison Type  : Divided
Filtered  : 1
Rank
description
Interaction Map
red
green
network_comparison
340 myelin gene expression factor 2. [refseq;acc:nm_016132] High confidence 235.383 258.476 1.09811
341 60s ribosomal protein l9. [swissprot;acc:p32969] 240.243 263.798 1.09805
kv channel interacting protein 1; vesicle apc-binding protein; a-type potassium channel modulatory protein 1. [refseq;acc:nm_014592] Low confidence 214.027 222.415 1.03919
342 40s ribosomal protein s20. [swissprot;acc:p17075] High confidence 243.5 267.21 1.09737
tho complex 3. [refseq;acc:nm_032361] Low confidence 186.383 179.374 1.03907
343 potassium channel-interacting protein 4 isoform 4; calsenilin-like protein. [refseq;acc:nm_147183] 213.982 222.326 1.03899
protein arginine n-methyltransferase 3 (ec 2.1.1.-) (fragment). [swissprot;acc:o60678] High confidence 241.625 265.136 1.0973
344 40s ribosomal protein s2 (s4) (llrep3 protein). [swissprot;acc:p15880]
mitochondrial ribosomal protein l44. [refseq;acc:nm_022915] Low confidence 216.283 208.173 1.03896
345 kv channel interacting protein 2 isoform 4; a-type potassium channel modulatory protein 2; cardiac voltage gated potassium channel modulatory subunit. [refseq;acc:nm_173193] 213.976 222.312
ump-cmp kinase (ec 2.7.4.14) (cytidylate kinase) (deoxycytidylate kinase) (cytidine monophosphate kinase). [swissprot;acc:p30085] High confidence 242.14 265.697 1.09729
346 40s ribosomal protein s3. [swissprot;acc:p23396] 241.612 265.119
dynein intermediate chain 2, cytosolic (dh ic-2) (cytoplasmic dynein intermediate chain 2). [swissprot;acc:q13409] Low confidence 209.221 201.38 1.03894
347 gtp:amp phosphotransferase mitochondrial (ec 2.7.4.10) (ak3) (adenylate kinase 3 alpha like 1). [swissprot;acc:q9uij7] High confidence 242.14 265.697 1.09729
nucleoside diphosphate kinase 7 (ec 2.7.4.6) (ndk 7) (ndp kinase 7) (nm23-h7). [swissprot;acc:q9y5b8] Low confidence 210.796 202.935 1.03874
348 adenylate kinase isoenzyme 4, mitochondrial (ec 2.7.4.3) (atp-amp transphosphorylase). [swissprot;acc:p27144] High confidence 242.14 265.696 1.09728
spartin; trans-activated by hepatitis c virus core protein 1. [refseq;acc:nm_015087] Low confidence 210.796 202.935 1.03874
349 adapter-related protein complex 2 alpha 2 subunit (alpha-adaptin c) (clathrin assembly protein complex 2 alpha-c large chain) (100 kda coated vesicle protein c) (plasma membrane adaptor ha2/ap2 adaptin alpha c subunit) (huntingtin-interacting protein hypj). [swissprot;acc:o94973] 204.762 197.135 1.03869
surfeit locus protein 5. [swissprot;acc:q15528] High confidence 242.14 265.696 1.09728
350 fuse-binding protein-interacting repressor isoform b; siah binding protein 1; pyrimidine tract binding splicing factor; ro ribonucleoprotein-binding protein 1; poly-u binding splicing factor puf60. [refseq;acc:nm_014281] Low confidence 204.762 197.135 1.03869
zinc finger protein 291. [swissprot;acc:q9by12] High confidence 242.14 265.696 1.09728
351 clathrin coat assembly protein ap17 (clathrin coat associated protein ap17) (plasma membrane adaptor ap-2 17 kda protein) (ha2 17 kda subunit) (clathrin assembly protein 2 small chain). [swissprot;acc:p53680] Low confidence 204.762 197.135 1.03869
peroxisome biogenesis factor 1 (peroxin-1) (peroxisome biogenesis disorder protein 1). [swissprot;acc:o43933] High confidence 242.14 265.696 1.09728
352 adapter-related protein complex 2 alpha 1 subunit (alpha-adaptin a) (adaptor protein complex ap-2 alpha-1 subunit) (clathrin assembly protein complex 2 alpha-a large chain) (100 kda coated vesicle protein a) (plasma membrane adaptor ha2/ap2 adaptin alpha a subunit). [swissprot;acc:o95782] Low confidence 204.762 197.135 1.03869
protein 1-4 (atp binding protein associated with cell differentiation). [swissprot;acc:o14530] High confidence 242.14 265.696 1.09728
353 rgs19-interacting protein 1 (gaip c-terminus interacting protein gipc) (rgs-gaip interacting protein) (tax interaction protein 2) (tip-2). [swissprot;acc:o14908] 231.73 211.252 1.09694
ubiquitin-conjugating enzyme e2 g1 (ec 6.3.2.19) (ubiquitin-protein ligase g1) (ubiquitin carrier protein g1) (e217k) (ubc7). [swissprot;acc:q99462] Low confidence 202.962 195.416 1.03862
354 conserved oligomeric golgi complex component 3 (vesicle docking protein sec34 homolog) (p94). [swissprot;acc:q96jb2] 206.433 198.781 1.03849
syntaxin 10 (syn10). [swissprot;acc:o60499] High confidence 234.691 257.442 1.09694
355 ribonuclease p protein subunit p30 (ec 3.1.26.5) (rnasep protein p30) (rnase p subunit 2). [swissprot;acc:p78346] Low confidence 202.542 210.311 1.03836
syntaxin 6. [swissprot;acc:o43752] High confidence 234.673 257.414 1.09691
356 60s ribosomal protein l10a (csa-19). [swissprot;acc:p53025] 243.24 266.796 1.09684
splicing factor 3a subunit 3 (spliceosome associated protein 61) (sap 61) (sf3a60). [swissprot;acc:q12874] Low confidence 202.387 194.949 1.03815
357 60s ribosomal protein l10 (qm protein) (tumor suppressor qm) (laminin receptor homolog). [swissprot;acc:p27635] High confidence 243.12 266.661 1.09683
splicing factor 3 subunit 1 (spliceosome associated protein 114) (sap 114) (sf3a120). [swissprot;acc:q15459] Low confidence 202.387 194.949 1.03815
358 molybdenum cofactor synthesis protein 2 large subunit (molybdopterin synthase large subunit) (mpt synthase large subunit) (mocs2b) (moco1- b). [swissprot;acc:o96007] 207.531 199.938 1.03798
ribosomal protein l10-like protein. [refseq;acc:nm_080746] High confidence 243.12 266.662 1.09683
359 60s ribosomal protein l4 (l1). [swissprot;acc:p36578] 239.277 262.434 1.09678
molybdenum cofactor synthesis protein 3 (molybdopterin synthase sulfurylase) (mpt synthase sulfurylase). [swissprot;acc:o95396] Low confidence 207.531 199.938 1.03798
360 protein transport protein sec61 gamma subunit. [swissprot;acc:p38384] High confidence 243.072 266.559 1.09663
secreted modular calcium-binding protein 1. [refseq;acc:nm_022137] Low confidence 204.231 196.773 1.0379
361 mitochondrial ribosomal protein l17; lyst-interacting protein lip2. [refseq;acc:nm_022061] High confidence 242.83 266.248 1.09644
prefoldin subunit 1. [swissprot;acc:o60925] Low confidence 204.231 196.773 1.0379
362 apical-like protein (apxl protein). [swissprot;acc:q13796] High confidence 231.492 211.136 1.09641
secreted modular calcium-binding protein 2; smooth muscle associated protein 2. [refseq;acc:nm_022138] Low confidence 204.231 196.773 1.0379
363 choline dehydrogenase. [refseq;acc:nm_018397]
shroom-related protein; f-actin-binding protein; likely ortholog of mouse shroom. [refseq;acc:nm_020859] High confidence 231.481 211.131 1.09639
364 dgcr14 protein (digeorge syndrome critical region 14) (es2 protein). [swissprot;acc:q96df8] Low confidence 212.235 204.495 1.03785
dna-directed rna polymerase ii 140 kda polypeptide (ec 2.7.7.6) (rna polymerase ii subunit 2) (rpb2). [swissprot;acc:p30876] High confidence 243.208 266.617 1.09625
365 60s ribosomal protein l36, mitochondrial precursor (l36mt) (brca1- interacting protein 1). [swissprot;acc:q9p0j6] 242.744 266.07 1.09609

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/