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 1901 to 1950 of 16578 in total
Value Type  : Ranked
Filtered  : 1
Rank
Hugo
description
Network Comparison Type
Interaction Map
red
green
network_comparison
476 FUCA1 tissue alpha-l-fucosidase precursor (ec 3.2.1.51) (alpha-l-fucosidase i) (alpha-l-fucoside fucohydrolase). [swissprot;acc:p04066] Divided Low confidence 202.271 195.742 1.03336
KCNA4 potassium voltage-gated channel subfamily a member 4 (potassium channel kv1.4) (hk1) (hpcn2) (hbk4) (hukii). [swissprot;acc:p22459] High confidence 226.681 210.814 1.07527
Subtracted 15.867
PRRX1 paired mesoderm homeobox protein 1 (prx-1) (paired related homeobox protein 1) (homeobox protein phox1). [swissprot;acc:p54821] Low confidence 194.41 201.036 6.626
477 ARHGEF7 rho guanine nucleotide exchange factor 7 (pak-interacting exchange factor beta) (beta-pix) (cool-1) (p85). [swissprot;acc:q14155] High confidence 220.183 236.015 15.832
HNRNPR heterogeneous nuclear ribonucleoprotein r (hnrnp r). [swissprot;acc:o43390] Divided Low confidence 203.823 197.249 1.03333
NIP7 saccharomyces cerevisiae nip7p homolog. [refseq;acc:nm_016101] High confidence 251.926 234.547 1.0741
SAMSN1 sam-domain protein samsn-1 (sam domain, sh3 domain and nuclear localisation signals protein 1). [swissprot;acc:q9nsi8] Subtracted Low confidence 204.278 210.893 6.615
478 BLVRB flavin reductase (ec 1.5.1.30) (fr) (nadph-dependent diaphorase) (nadph-flavin reductase) (flr) (biliverdin reductase b) (ec 1.3.1.24) (bvr-b) (biliverdin-ix beta-reductase) (green heme binding protein) (ghbp). [swissprot;acc:p30043] Divided 207.68 214.591 1.03328
BRF1 transcription factor iiib 90 kda subunit (tfiiib90) (htfiiib90) (b- related factor 1) (hbrf) (tata box-binding protein-associated factor, rna polymerase iii, subunit 2) (taf3b2). [swissprot;acc:q92994] High confidence 228.051 212.321 1.07409
PAK2 serine/threonine-protein kinase pak 2 (ec 2.7.1.-) (p21-activated kinase 2) (pak-2) (pak65) (gamma-pak) (s6/h4 kinase). [swissprot;acc:q13177] Subtracted 220.171 235.979 15.808
SASH1 sam and sh3 domain containing 1. [refseq;acc:nm_015278] Low confidence 204.276 210.886 6.61
479 ARRB2 beta-arrestin 2 (arrestin, beta 2). [swissprot;acc:p32121] 194.137 187.552 6.585
COG5 conserved oligomeric golgi complex subunit 5 (13s golgi transport complex 90 kda subunit) (gtc-90) (golgi transport complex 1). [swissprot;acc:q9up83] High confidence 220.172 235.98 15.808
NOLA1 nucleolar protein family a, member 1; gar1 protein. [refseq;acc:nm_018983] Divided 228.051 212.321 1.07409
VTA1 protein c6orf55 (dopamine responsive protein drg-1) (my012 protein) (hspc228). [swissprot;acc:q9np79] Low confidence 207.68 214.591 1.03328
480 C15orf15 ribosomal protein l24-like; 60s ribosomal protein l30 isolog; my024 protein; homolog of yeast ribosomal like protein 24. [refseq;acc:nm_016304] Subtracted 206.763 200.18 6.583
NETO2 neuropilin- and tolloid-like protein 2 precursor. [refseq;acc:nm_018092] Divided High confidence 237.109 254.667 1.07405
PAK1 serine/threonine-protein kinase pak 1 (ec 2.7.1.-) (p21-activated kinase 1) (pak-1) (p65-pak) (alpha-pak). [swissprot;acc:q13153] Subtracted 220.172 235.98 15.808
SYNCRIP ns1-associated protein 1. [refseq;acc:nm_006372] Divided Low confidence 203.822 197.259 1.03327
481 HNRNPR heterogeneous nuclear ribonucleoprotein r (hnrnp r). [swissprot;acc:o43390] Subtracted 203.823 197.249 6.574
NETO1 neuropilin- and tolloid-like protein 1 isoform 3 precursor. [refseq;acc:nm_138966] Divided High confidence 237.109 254.667 1.07405
PAK3 serine/threonine-protein kinase pak 3 (ec 2.7.1.-) (p21-activated kinase 3) (pak-3) (beta-pak) (oligophrenin-3). [swissprot;acc:o75914] Subtracted 220.171 235.979 15.808
RRAGA ras-related gtp binding a; ras-related gtp-binding protein. [refseq;acc:nm_006570] Divided Low confidence 171.564 166.045 1.03324
482 ARHGEF6 rho guanine nucleotide exchange factor 6 (pak-interacting exchange factor alpha) (alpha-pix) (cool-2). [swissprot;acc:q15052] Subtracted High confidence 220.161 235.95 15.789
HNRNPU heterogenous nuclear ribonucleoprotein u (hnrnp u) (scaffold attachment factor a) (saf-a). [swissprot;acc:q00839] Divided 237.109 254.667 1.07405
PLRG1 pleiotropic regulator 1 (prl1homolog, arabidopsis); pleiotropic regulator 1 (prl1, arabidopsis homolog). [refseq;acc:nm_002669] Subtracted Low confidence 201.847 195.283 6.564
TRIP12 thyroid receptor interacting protein 12 (trip12). [swissprot;acc:q14669] Divided 204.65 198.086 1.03314
483 no value rna-binding protein. [refseq;acc:nm_019027] 203.821 197.289 1.03311
BRF1 transcription factor iiib 90 kda subunit (tfiiib90) (htfiiib90) (b- related factor 1) (hbrf) (tata box-binding protein-associated factor, rna polymerase iii, subunit 2) (taf3b2). [swissprot;acc:q92994] Subtracted High confidence 228.051 212.321 15.73
RUNX2 runt-related transcription factor 2 (core-binding factor, alpha 1 subunit) (cbf-alpha 1) (acute myeloid leukemia 3 protein) (oncogene aml-3) (polyomavirus enhancer binding protein 2 alpha a subunit) (pebp2-alpha a) (pea2-alpha a) (sl3-3 enhancer factor 1 alpha a subunit) (sl3/akv core-binding factor alpha a subunit) (osteoblast- specific transcription factor 2) (osf-2). [swissprot;acc:q13950] Divided 237.109 254.667 1.07405
TRIP12 thyroid receptor interacting protein 12 (trip12). [swissprot;acc:q14669] Subtracted Low confidence 204.65 198.086 6.564
484 no value apobec-1 complementation factor isoform 1; apobec-1 stimulating protein; apo-b rna editing protein. [refseq;acc:nm_014576] Divided 203.821 197.291 1.0331
HNRPUL1 e1b-55kda-associated protein 5 isoform a. [refseq;acc:nm_007040] High confidence 237.109 254.667 1.07405
NOLA1 nucleolar protein family a, member 1; gar1 protein. [refseq;acc:nm_018983] Subtracted 228.051 212.321 15.73
SYNCRIP ns1-associated protein 1. [refseq;acc:nm_006372] Low confidence 203.822 197.259 6.563
485 BRPF1 tubulin tyrosine ligase-like protein hottl (hqp0207). [swissprot;acc:q9y4r7] Divided 205.109 198.551 1.03303
Subtracted 6.558
PPM1B protein phosphatase 2c beta isoform (ec 3.1.3.16) (pp2c-beta). [swissprot;acc:o75688] High confidence 231.276 215.627 15.649
RPL18 60s ribosomal protein l18. [swissprot;acc:q07020] Divided 237.109 254.667 1.07405
486 CXorf9 chromosome x open reading frame 9; likely ortholog of mouse sh3 gene sly. [refseq;acc:nm_018990] Low confidence 204.331 211.075 1.03301
EEF1B2 elongation factor 1-beta (ef-1-beta). [swissprot;acc:p24534] Subtracted 206.154 199.596 6.558
EIF6 eukaryotic translation initiation factor 6 (eif-6) (b4 integrin interactor) (cab) (p27(bbp)) (b(2)gcn homolog). [swissprot;acc:p56537] High confidence 248.866 233.287 15.579
MCTS1 mct-1 protein. [refseq;acc:nm_014060] Divided 226.313 243.03 1.07387
487 ARRB1 beta-arrestin 1 (arrestin, beta 1). [swissprot;acc:p49407] Subtracted Low confidence 194.237 187.689 6.548
C15orf15 ribosomal protein l24-like; 60s ribosomal protein l30 isolog; my024 protein; homolog of yeast ribosomal like protein 24. [refseq;acc:nm_016304] Divided 206.763 200.18 1.03289
MDH2 malate dehydrogenase, mitochondrial precursor (ec 1.1.1.37). [swissprot;acc:p40926] Subtracted High confidence 238.529 254.099 15.57
MRPL22 mitochondrial ribosomal protein l22. [refseq;acc:nm_014180] Divided 226.313 243.03 1.07387
488 no value gaba-a receptor-associated protein. [sptrembl;acc:q9by60] Subtracted 82.5916 98.0548 15.4632
PCNA proliferating cell nuclear antigen (pcna) (cyclin). [swissprot;acc:p12004] Low confidence 207.84 201.297 6.543

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/