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 - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.


Navigation/Query Panel:
Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].
Rank Gene Network Comparison Type Hugo description Value Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 1880 to 1929 of 16578 in total
Value Type  : Ranked
Filtered  : 1
Rank
Network Comparison Type
Hugo
description
Interaction Map
red
green
network_comparison
470 Subtracted TMOD1 tropomodulin 1 (erythrocyte tropomodulin) (e-tmod). [swissprot;acc:p28289] Low confidence 209.136 202.478 6.658
471 Divided LAMC1 laminin gamma-1 chain precursor (laminin b2 chain). [swissprot;acc:p11047] High confidence 248.152 267.226 1.07686
RBM39 rna-binding region containing protein 2 (hepatocellular carcinoma protein 1) (splicing factor hcc1). [swissprot;acc:q14498] Low confidence 208.29 201.499 1.0337
Subtracted SNX9 sorting nexin 9 (sh3 and px domain-containing protein 1) (sdp1 protein). [swissprot;acc:q9y5x1] 209.136 202.478 6.658
ZNF622 zinc finger-like protein 9. [refseq;acc:nm_033414] High confidence 250.942 235.004 15.938
472 Divided PLRG1 pleiotropic regulator 1 (prl1homolog, arabidopsis); pleiotropic regulator 1 (prl1, arabidopsis homolog). [refseq;acc:nm_002669] Low confidence 201.847 195.283 1.03361
SLC46A2 thymic stromal co-transporter. [refseq;acc:nm_033051] High confidence 248.152 267.226 1.07686
Subtracted SLC45A2 membrane-associated transporter protein (aim-1 protein) (melanoma antigen aim1). [swissprot;acc:q9umx9] 250.942 235.004 15.938
TMOD2 neuronal tropomodulin (n-tmod) (tropomodulin 2). [swissprot;acc:q9nzr1] Low confidence 209.136 202.478 6.658
473 Divided EXOC1 exocyst complex component sec3 (bm-012). [swissprot;acc:q9nv70] 209.111 202.34 1.03346
PRPF31 pre-mrna processing factor 31 homolog; pre-mrna processing factor 31 homolog (yeast). [refseq;acc:nm_015629] High confidence 225.661 209.651 1.07637
Subtracted no value guanine nucleotide-binding protein-like 1 (gtp-binding protein hsr1). [swissprot;acc:p36915] 250.942 235.004 15.938
TNK2 activated p21cdc42hs kinase. [refseq;acc:nm_005781] Low confidence 209.136 202.478 6.658
474 Divided KCNA2 potassium voltage-gated channel subfamily a member 2 (potassium channel kv1.2) (rbk2) (hbk5) (ngk1) (mk2) (hukiv). [swissprot;acc:p16389] High confidence 226.789 210.818 1.07576
RRAGB ras-related gtp binding b short isoform; gtp-binding protein ragb. [refseq;acc:nm_006064] Low confidence 171.213 165.68 1.0334
Subtracted KCNA1 potassium voltage-gated channel subfamily a member 1 (potassium channel kv1.1) (huki) (hbk1). [swissprot;acc:q09470] High confidence 226.727 210.816 15.911
PRPF40B huntingtin interacting protein c. [refseq;acc:nm_012272] Low confidence 201.429 194.776 6.653
475 Divided FUCA2 fucosidase, alpha-l- 2, plasma. [refseq;acc:nm_032020] 202.311 195.778 1.03337
KCNA1 potassium voltage-gated channel subfamily a member 1 (potassium channel kv1.1) (huki) (hbk1). [swissprot;acc:q09470] High confidence 226.727 210.816 1.07547
Subtracted MEMO1P protein cgi-27 (c21orf19-like protein). [swissprot;acc:q9y316] 236.964 252.86 15.896
SLC7A5 large neutral amino acids transporter small subunit 1 (l-type amino acid transporter 1) (4f2 light chain) (4f2 lc) (4f2lc) (cd98 light chain) (integral membrane protein e16) (hlat1). [swissprot;acc:q01650] Low confidence 201.466 194.819 6.647
476 Divided FUCA1 tissue alpha-l-fucosidase precursor (ec 3.2.1.51) (alpha-l-fucosidase i) (alpha-l-fucoside fucohydrolase). [swissprot;acc:p04066] 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 Divided HNRNPR heterogeneous nuclear ribonucleoprotein r (hnrnp r). [swissprot;acc:o43390] 203.823 197.249 1.03333
NIP7 saccharomyces cerevisiae nip7p homolog. [refseq;acc:nm_016101] High confidence 251.926 234.547 1.0741
Subtracted ARHGEF7 rho guanine nucleotide exchange factor 7 (pak-interacting exchange factor beta) (beta-pix) (cool-1) (p85). [swissprot;acc:q14155] 220.183 236.015 15.832
SAMSN1 sam-domain protein samsn-1 (sam domain, sh3 domain and nuclear localisation signals protein 1). [swissprot;acc:q9nsi8] Low confidence 204.278 210.893 6.615
478 Divided 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] 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
Subtracted 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] 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 Divided NOLA1 nucleolar protein family a, member 1; gar1 protein. [refseq;acc:nm_018983] High confidence 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
Subtracted 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
480 Divided NETO2 neuropilin- and tolloid-like protein 2 precursor. [refseq;acc:nm_018092] 237.109 254.667 1.07405
SYNCRIP ns1-associated protein 1. [refseq;acc:nm_006372] Low confidence 203.822 197.259 1.03327
Subtracted C15orf15 ribosomal protein l24-like; 60s ribosomal protein l30 isolog; my024 protein; homolog of yeast ribosomal like protein 24. [refseq;acc:nm_016304] 206.763 200.18 6.583
PAK1 serine/threonine-protein kinase pak 1 (ec 2.7.1.-) (p21-activated kinase 1) (pak-1) (p65-pak) (alpha-pak). [swissprot;acc:q13153] High confidence 220.172 235.98 15.808
481 Divided NETO1 neuropilin- and tolloid-like protein 1 isoform 3 precursor. [refseq;acc:nm_138966] 237.109 254.667 1.07405
RRAGA ras-related gtp binding a; ras-related gtp-binding protein. [refseq;acc:nm_006570] Low confidence 171.564 166.045 1.03324
Subtracted HNRNPR heterogeneous nuclear ribonucleoprotein r (hnrnp r). [swissprot;acc:o43390] 203.823 197.249 6.574
PAK3 serine/threonine-protein kinase pak 3 (ec 2.7.1.-) (p21-activated kinase 3) (pak-3) (beta-pak) (oligophrenin-3). [swissprot;acc:o75914] High confidence 220.171 235.979 15.808
482 Divided HNRNPU heterogenous nuclear ribonucleoprotein u (hnrnp u) (scaffold attachment factor a) (saf-a). [swissprot;acc:q00839] 237.109 254.667 1.07405
TRIP12 thyroid receptor interacting protein 12 (trip12). [swissprot;acc:q14669] Low confidence 204.65 198.086 1.03314
Subtracted ARHGEF6 rho guanine nucleotide exchange factor 6 (pak-interacting exchange factor alpha) (alpha-pix) (cool-2). [swissprot;acc:q15052] High confidence 220.161 235.95 15.789
PLRG1 pleiotropic regulator 1 (prl1homolog, arabidopsis); pleiotropic regulator 1 (prl1, arabidopsis homolog). [refseq;acc:nm_002669] Low confidence 201.847 195.283 6.564
483 Divided no value rna-binding protein. [refseq;acc:nm_019027] 203.821 197.289 1.03311

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/