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 Network Comparison Type Value Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 1325 to 1374 of 16578 in total
Value Type  : Ranked
Filtered  : 1
Rank
Hugo
description
Network Comparison Type
Interaction Map
red
green
network_comparison
332 DYNC1I1 dynein intermediate chain 1, cytosolic (dh ic-1) (cytoplasmic dynein intermediate chain 1). [swissprot;acc:o14576] Divided Low confidence 209.495 201.474 1.03981
NEDD9 enhancer of filamentation 1 (hef1) (crk-associated substrate-related protein) (cas-l) (casl) (pp105) (neural precursor cell expressed developmentally down-regulated 9). [swissprot;acc:q14511] Subtracted High confidence 224.633 203.251 21.382
NEUROD6 neurogenic differentiation factor 6 (neurod6) (my051 protein). [swissprot;acc:q96nk8] Divided 312 284 1.09859
SPG20 spartin; trans-activated by hepatitis c virus core protein 1. [refseq;acc:nm_015087] Subtracted Low confidence 210.796 202.935 7.861
333 no value transcription factor dp-1 (e2f dimerization partner 1) (drtf1- polypeptide-1) (drtf1). [swissprot;acc:q14186] High confidence 265.634 244.304 21.33
C20orf43 protein c20orf43 (hspc164/hspc169) (ad-007) (cda05). [swissprot;acc:q9by42] Divided Low confidence 200.482 208.446 1.03972
DYNC1I2 dynein intermediate chain 2, cytosolic (dh ic-2) (cytoplasmic dynein intermediate chain 2). [swissprot;acc:q13409] Subtracted 209.221 201.38 7.841
NEUROD1 neurogenic differentiation factor 1 (neurod1) (neurod). [swissprot;acc:q13562] Divided High confidence 312 284 1.09859
334 BICD2 coiled-coil protein bicd2; homolog of drosophila bicaudal d. [refseq;acc:nm_015250] Low confidence 202.616 194.878 1.03971
NEUROD4 neurogenic differentiation factor 4 (neurod4). [swissprot;acc:q9hd90] High confidence 312 284 1.09859
RRM2B ribonucleotide reductase m2 b (tp53 inducible); p53-inducible ribonucleotide reductase small subunit 2 homolog. [refseq;acc:nm_015713] Subtracted 232.473 211.207 21.266
STT3B source of immunodominant mhc-associated peptides; homolog of yeast stt3 gene. [refseq;acc:nm_178862] Low confidence 199.905 192.123 7.782
335 BICD1 bicaudal d homolog 1; bicaudal-d, drosophila, homolog of, 1. [refseq;acc:nm_001714] Divided 202.616 194.878 1.03971
CHD5 chromodomain helicase dna binding protein 5. [refseq;acc:nm_015557] High confidence 312 284 1.09859
RPP30 ribonuclease p protein subunit p30 (ec 3.1.26.5) (rnasep protein p30) (rnase p subunit 2). [swissprot;acc:p78346] Subtracted Low confidence 202.542 210.311 7.769
SCYE1 multisynthetase complex auxiliary component p43 [contains: endothelial-monocyte activating polypeptide ii (emap-ii) (small inducible cytokine subfamily e member 1)]. [swissprot;acc:q12904] High confidence 223.273 202.423 20.85
336 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] Divided 312 284 1.09859
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] Subtracted Low confidence 199.343 191.59 7.753
POLR1E rna polymerase i associated factor 53. [refseq;acc:nm_022490] High confidence 241.045 261.874 20.829
TFIP11 tuftelin-interacting protein 11 (hspc006). [swissprot;acc:q9ubb9] Divided Low confidence 202.616 194.878 1.03971
337 no value 60s ribosomal protein l12. [swissprot;acc:p30050] High confidence 243.583 267.527 1.0983
CDKL1 serine/threonine-protein kinase kkialre (ec 2.7.1.-) (cyclin-dependent kinase-like 1). [swissprot;acc:q00532] Low confidence 201.873 194.181 1.03961
DGCR14 dgcr14 protein (digeorge syndrome critical region 14) (es2 protein). [swissprot;acc:q96df8] Subtracted 212.235 204.495 7.74
STT3B source of immunodominant mhc-associated peptides; homolog of yeast stt3 gene. [refseq;acc:nm_178862] High confidence 200.691 179.88 20.811
338 no value 60s ribosomal protein l12 like protein. [sptrembl;acc:o60886] Divided 243.583 267.528 1.0983
BICD2 coiled-coil protein bicd2; homolog of drosophila bicaudal d. [refseq;acc:nm_015250] Subtracted Low confidence 202.616 194.878 7.738
STT3A oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [swissprot;acc:p46977] 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

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/