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 Hugo description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 1351 to 1400 of 16578 in total
Value Type  : Ranked
Filtered  : 1
Rank
Hugo
description
Network Comparison Type
Interaction Map
red
green
network_comparison
338 STT3A oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [swissprot;acc:p46977] Subtracted High confidence 200.691 179.88 20.811
TXNL4A spliceosomal u5 snrnp-specific 15 kda protein (dim1 protein homolog) (thioredoxin-like u5 snrnp protein u5-15kd). [swissprot;acc:o14834] Divided Low confidence 202.572 194.86 1.03958
339 no value dj999l4.1 (novel protein similar to ribosomal protein l12 (rpl12)). [sptrembl;acc:q9nq02] High confidence 243.583 267.527 1.0983
BICD1 bicaudal d homolog 1; bicaudal-d, drosophila, homolog of, 1. [refseq;acc:nm_001714] Subtracted Low confidence 202.616 194.878 7.738
DDOST dolichyl-diphosphooligosaccharide--protein glycosyltransferase 48 kda subunit precursor (ec 2.4.1.119) (oligosaccharyl transferase 48 kda subunit) (ddost 48 kda subunit). [swissprot;acc:p39656] High confidence 200.691 179.88 20.811
GGPS1 geranylgeranyl pyrophosphate synthetase (ggpp synthetase) (ggppsase) (geranylgeranyl diphosphate synthase) [includes: dimethylallyltransferase (ec 2.5.1.1); geranyltranstransferase (ec 2.5.1.10); farnesyltranstransferase (ec 2.5.1.29)]. [swissprot;acc:o95749] Divided Low confidence 209.518 201.554 1.03951
340 BET1L blocked early in transport 1 homolog (s. cerevisiae) like; golgi snare 15 kda protein. [refseq;acc:nm_016526] 201.827 194.178 1.03939
MRPS9 28s ribosomal protein s9, mitochondrial precursor (mrp-s9). [swissprot;acc:p82933] Subtracted High confidence 239.75 260.544 20.794
MYEF2 myelin gene expression factor 2. [refseq;acc:nm_016132] Divided 235.383 258.476 1.09811
TFIP11 tuftelin-interacting protein 11 (hspc006). [swissprot;acc:q9ubb9] Subtracted Low confidence 202.616 194.878 7.738
341 no value 60s ribosomal protein l9. [swissprot;acc:p32969] Divided High confidence 240.243 263.798 1.09805
KCNIP1 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
UBE1C ubiquitin-activating enzyme e1c (uba3 homolog, yeast); ubiquitin-activating enzyme e1c (homologous to yeast uba3). [refseq;acc:nm_003968] Subtracted 192.088 184.374 7.714
UQCRFSL1 ubiquinol-cytochrome c reductase iron-sulfur subunit, mitochondrial precursor (ec 1.10.2.2) (rieske iron-sulfur protein) (risp). [swissprot;acc:p47985] High confidence 240.788 261.416 20.628
342 no value tho complex 3. [refseq;acc:nm_032361] Divided Low confidence 186.383 179.374 1.03907
GALE udp-glucose 4-epimerase (ec 5.1.3.2) (galactowaldenase) (udp- galactose 4-epimerase). [swissprot;acc:q14376] Subtracted 200.249 192.535 7.714
POLR1C dna-directed rna polymerase i 40 kda polypeptide (ec 2.7.7.6) (rpa40) (rpa39). [swissprot;acc:o15160] High confidence 240.913 261.45 20.537
RPS20 40s ribosomal protein s20. [swissprot;acc:p17075] Divided 243.5 267.21 1.09737
343 GIPC1 rgs19-interacting protein 1 (gaip c-terminus interacting protein gipc) (rgs-gaip interacting protein) (tax interaction protein 2) (tip-2). [swissprot;acc:o14908] Subtracted 231.73 211.252 20.478
KCNIP4 potassium channel-interacting protein 4 isoform 4; calsenilin-like protein. [refseq;acc:nm_147183] Divided Low confidence 213.982 222.326 1.03899
PRMT3 protein arginine n-methyltransferase 3 (ec 2.1.1.-) (fragment). [swissprot;acc:o60678] High confidence 241.625 265.136 1.0973
TXNL4A spliceosomal u5 snrnp-specific 15 kda protein (dim1 protein homolog) (thioredoxin-like u5 snrnp protein u5-15kd). [swissprot;acc:o14834] Subtracted Low confidence 202.572 194.86 7.712
344 no value 40s ribosomal protein s2 (s4) (llrep3 protein). [swissprot;acc:p15880] Divided High confidence 241.625 265.136 1.0973
CDKL1 serine/threonine-protein kinase kkialre (ec 2.7.1.-) (cyclin-dependent kinase-like 1). [swissprot;acc:q00532] Subtracted Low confidence 201.873 194.181 7.692
MRPL44 mitochondrial ribosomal protein l44. [refseq;acc:nm_022915] Divided 216.283 208.173 1.03896
POLR1B dna-directed rna polymerase i 135 kda polypeptide (ec 2.7.7.6) (rna polymerase i subunit 2) (rpa135). [swissprot;acc:q9h9y6] Subtracted High confidence 240.6 261.041 20.441
345 no value splicing factor 3b subunit 3 (spliceosome associated protein 130) (sap 130) (sf3b130) (pre-mrna splicing factor sf3b 130 kda subunit). [swissprot;acc:q15393] 224.445 204.044 20.401
CMPK ump-cmp kinase (ec 2.7.4.14) (cytidylate kinase) (deoxycytidylate kinase) (cytidine monophosphate kinase). [swissprot;acc:p30085] Divided 242.14 265.697 1.09729
EGFL8 palmitoyl-protein thioesterase 2 precursor (ec 3.1.2.22) (palmitoyl- protein hydrolase 2) (ppt-2) (g14). [swissprot;acc:q9umr5] Subtracted Low confidence 214.628 222.301 7.673
KCNIP2 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] Divided 213.976 222.312 1.03896
346 COG3 conserved oligomeric golgi complex component 3 (vesicle docking protein sec34 homolog) (p94). [swissprot;acc:q96jb2] Subtracted 206.433 198.781 7.652
DYNC1I2 dynein intermediate chain 2, cytosolic (dh ic-2) (cytoplasmic dynein intermediate chain 2). [swissprot;acc:q13409] Divided 209.221 201.38 1.03894
RPS3 40s ribosomal protein s3. [swissprot;acc:p23396] High confidence 241.612 265.119 1.09729
SHROOM2 apical-like protein (apxl protein). [swissprot;acc:q13796] Subtracted 231.492 211.136 20.356
347 AK3 gtp:amp phosphotransferase mitochondrial (ec 2.7.4.10) (ak3) (adenylate kinase 3 alpha like 1). [swissprot;acc:q9uij7] Divided 242.14 265.697 1.09729
BET1L blocked early in transport 1 homolog (s. cerevisiae) like; golgi snare 15 kda protein. [refseq;acc:nm_016526] Subtracted Low confidence 201.827 194.178 7.649
NME7 nucleoside diphosphate kinase 7 (ec 2.7.4.6) (ndk 7) (ndp kinase 7) (nm23-h7). [swissprot;acc:q9y5b8] Divided 210.796 202.935 1.03874
SHROOM3 shroom-related protein; f-actin-binding protein; likely ortholog of mouse shroom. [refseq;acc:nm_020859] Subtracted High confidence 231.481 211.131 20.35
348 no value adenylate kinase isoenzyme 4, mitochondrial (ec 2.7.4.3) (atp-amp transphosphorylase). [swissprot;acc:p27144] Divided 242.14 265.696 1.09728
SLC15A2 oligopeptide transporter, kidney isoform (peptide transporter 2) (kidney h+/peptide cotransporter) (solute carrier family 15, member 2). [swissprot;acc:q16348] Subtracted 185.969 165.623 20.346
SPG20 spartin; trans-activated by hepatitis c virus core protein 1. [refseq;acc:nm_015087] Divided Low confidence 210.796 202.935 1.03874
TRAPPC3 bet3 homolog. [swissprot;acc:o43617] Subtracted 197.221 189.574 7.647
349 AP2A2 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] Divided 204.762 197.135 1.03869
Subtracted 7.627
CEBPZ ccaat-box-binding transcription factor (ccaat-binding factor) (cbf). [swissprot;acc:q03701] High confidence 255.112 234.804 20.308
MED22 surfeit locus protein 5. [swissprot;acc:q15528] Divided 242.14 265.696 1.09728
350 no value tfiih basal transcription factor complex p44 subunit (basic transcription factor 2 44 kda subunit) (btf2-p44) (general transcription factor iih polypeptide 2). [swissprot;acc:q13888] Subtracted 233.376 253.539 20.163
PUF60 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] Divided Low confidence 204.762 197.135 1.03869
Subtracted 7.627
SCAPER zinc finger protein 291. [swissprot;acc:q9by12] Divided High confidence 242.14 265.696 1.09728

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/