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 Network Type I Analysis

Type 1 network in which we propagated the absolute log regulation ratio abs(log(r/g)). We used the filtered lowest boundary of the confidence interval for the microarray measurement based and used the high confidence interaction map. Because type-I networks tend to favour highly connected proteins we tested a normalisation scheme in which we would run the network once with real values (the measured column) and once with simulated values where each measured point is set to 1 instead of the actual signal (the expected column). Afterwards we divided the measured value by the expected value. This normalisation scheme works to a certain extend but will lead to a variance that is directly related to the connectivity of each protein. In the end we dropped the use of Type-I networks due to the many technical problems they pose.


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Gene Rank expected description measured final Hugo
Results: HTML CSV LaTeX Showing element 501 to 550 of 3206 in total
Rank
expected
description
measured
final
Hugo
501 1.0262 SPECTRIN SH3 DOMAIN BINDING PROTEIN 1; EPS8 BINDING PROTEIN; INTERACTOR PROTEIN ABLBP4; ABL-INTERACTOR PROTEIN 1 LONG; NAP1 BINDING PROTEIN. [RefSeq;Acc:NM_005470] 0.281309 0.274126876 ABI1
502 0.146476 0.0401445 0.274068789 CDV3
503 1.33921 EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT 7 (EIF-3 ZETA) (EIF3 P66) (EIF3D). [SWISSPROT;Acc:O15371] 0.367035 0.274068294 EIF3D
504 0.104626 ENIGMA PROTEIN; LIM DOMAIN PROTEIN. [RefSeq;Acc:NM_005451] 0.0286746 0.274067631 no value
505 0.66836 INOSINE-5'-MONOPHOSPHATE DEHYDROGENASE 1 (EC 1.1.1.205) (IMP DEHYDROGENASE 1) (IMPDH-I) (IMPD 1). [SWISSPROT;Acc:P20839] 0.183159 0.274042432 IMPDH1
506 0.574482 INOSINE-5'-MONOPHOSPHATE DEHYDROGENASE 2 (EC 1.1.1.205) (IMP DEHYDROGENASE 2) (IMPDH-II) (IMPD 2). [SWISSPROT;Acc:P12268] 0.157432 0.274041658 IMPDH2
507 1.27232 GMP SYNTHASE [GLUTAMINE-HYDROLYZING] (EC 6.3.5.2) (GLUTAMINE AMIDOTRANSFERASE) (GMP SYNTHETASE). [SWISSPROT;Acc:P49915] 0.348668 0.274041122 GMPS
508 0.493083 HEAT SHOCK FACTOR BINDING PROTEIN 1. [SWISSPROT;Acc:O75506] 0.135095 0.273980243 no value
509 0.353554 "RNA, U TRANSPORTER 1; SNURPORTIN-1. [RefSeq;Acc:NM_005701]" 0.0968147 0.273832852 SNUPN
510 0.914445 0.250323 0.27374309 KIAA1217
511 0.482648 PROTEIN KINASE CLK2 (EC 2.7.1.-) (CDC-LIKE KINASE 2). [SWISSPROT;Acc:P49760] 0.131932 0.273350351 CLK2
512 0.367745 PROTEIN KINASE CLK3 (EC 2.7.1.-) (CDC-LIKE KINASE 3). [SWISSPROT;Acc:P49761] 0.1005 0.273287196 CLK3
513 1.98406 NUCLEAR PROTEIN SKIP (SKI-INTERACTING PROTEIN) (SNW1 PROTEIN) (NUCLEAR RECEPTOR COACTIVATOR NCOA-62). [SWISSPROT;Acc:Q13573] 0.541777 0.273064827 SNW1
514 1.55794 RNA-BINDING PROTEIN 9 (RNA BINDING MOTIF PROTEIN 9) (HEXARIBONUCLEOTIDE BINDING PROTEIN 2) (REPRESSOR OF TAMOXIFEN TRANSCRIPTIONAL ACTIVITY). [SWISSPROT;Acc:O43251] 0.424547 0.27250536 RBM9
515 1.96129 ATAXIN 2-BINDING PROTEIN. [SWISSPROT;Acc:Q9NWB1] 0.534301 0.272423252 no value
516 0.176368 0.0480412 0.272391817 METT10D
517 1.15171 0.313715 0.272390619 UBAP2L
518 1.8743 M-PHASE INDUCER PHOSPHATASE 2 (EC 3.1.3.48) (DUAL SPECIFICITY PHOSPHATASE CDC25B). [SWISSPROT;Acc:P30305] 0.510382 0.272305394 CDC25B
519 0.139495 "BREAST CARCINOMA AMPLIFIED SEQUENCE 2; SPLICEOSOME ASSOCIATED PROTEIN, AMPLIFIED IN BREAST CANCER. [RefSeq;Acc:NM_005872]" 0.0379775 0.272249901 BCAS2
520 1.2232 "CDC5-LIKE; CDC5 (CELL DIVISION CYCLE 5, S. POMBE, HOMOLOG)-LIKE; CELL DIVISION CYCLE 5, S. POMBE, HOMOLOG-LIKE; CDC5-RELATED PROTEIN. [RefSeq;Acc:NM_001253]" 0.333016 0.272249836 CDC5L
521 1.85404 RNA-BINDING PROTEIN WITH MULTIPLE SPLICING (RBP-MS). [SWISSPROT;Acc:Q93062] 0.504359 0.272032426 RBPMS
522 2.5522 "PRE-MRNA CLEAVAGE FACTOR I, 59 KDA SUBUNIT. [RefSeq;Acc:NM_024811]" 0.694134 0.271974767 no value
523 0.525483 "1,4-ALPHA-GLUCAN BRANCHING ENZYME (EC 2.4.1.18) (GLYCOGEN BRANCHING ENZYME) (BRANCHER ENZYME). [SWISSPROT;Acc:Q04446]" 0.142881 0.271904134 GBE1
524 0.0845876 "GLYCOGEN PHOSPHORYLASE, MUSCLE FORM (EC 2.4.1.1) (MYOPHOSPHORYLASE). [SWISSPROT;Acc:P11217]" 0.0229997 0.27190392 PYGM
525 0.0851144 "GLYCOGEN PHOSPHORYLASE, BRAIN FORM (EC 2.4.1.1). [SWISSPROT;Acc:P11216]" 0.0231429 0.271903462 PYGB
526 0.0916194 MYOSIN XV (UNCONVENTIONAL MYOSIN-15). [SWISSPROT;Acc:Q9UKN7] 0.0249116 0.271903112 MYO15A
527 "GLYCOGEN PHOSPHORYLASE, LIVER FORM (EC 2.4.1.1). [SWISSPROT;Acc:P06737]" PYGL
528 1.13987 "PROTEIN PHOSPHATASE 1, REGULATORY (INHIBITOR) SUBUNIT 12B ISOFORM A; MYOSIN PHOSPHATASE REGULATORY SUBUNIT; MYOSIN PHOSPHATASE, TARGET SUBUNIT 2. [RefSeq;Acc:NM_002481]" 0.309836 0.271816962 PPP1R12B
529 0.933978 "PROTEIN PHOSPHATASE 1, REGULATORY (INHIBITOR) SUBUNIT 12A; MYOSIN PHOSPHATASE, TARGET SUBUNIT 1. [RefSeq;Acc:NM_002480]" 0.253813 0.271754795 PPP1R12A
530 0.957852 0.260139 0.271585798 RBM24
531 0.797256 RNA-BINDING REGION CONTAINING PROTEIN 1 (HSRNASEB) (SSDNA BINDING PROTEIN SEB4) (CLL-ASSOCIATED ANTIGEN KW-5). [SWISSPROT;Acc:Q9H0Z9] 0.216511 0.271570236 RBM38
532 1.49189 "KARYOPHERIN BETA 2B, TRANSPORTIN; IMPORTIN 3. [RefSeq;Acc:NM_013433]" 0.404881 0.271387971 TNPO2
533 0.856628 SMALL NUCLEAR RIBONUCLEOPROTEIN F (SNRNP-F) (SM PROTEIN F) (SM-F) (SMF). [SWISSPROT;Acc:Q15356] 0.232461 0.271367501 SNRPF
534 0.14739 SMALL NUCLEAR RIBONUCLEOPROTEIN E (SNRNP-E) (SM PROTEIN E) (SM-E) (SME). [SWISSPROT;Acc:P08578] 0.0399967 0.271366443 no value
535 1.63446 IMPORTIN BETA-2 SUBUNIT (KARYOPHERIN BETA-2 SUBUNIT) (TRANSPORTIN) (M9 REGION INTERACTION PROTEIN) (MIP). [SWISSPROT;Acc:Q92973] 0.443276 0.271206392 TNPO1
536 0.450566 BROMODOMAIN-CONTAINING PROTEIN 3 (RING3-LIKE PROTEIN). [SWISSPROT;Acc:Q15059] 0.122154 0.271112334 BRD3
537 0.390223 BROMODOMAIN-CONTAINING PROTEIN 2 (RING3 PROTEIN) (O27.1.1). [SWISSPROT;Acc:P25440] 0.105783 0.271083457 BRD2
538 0.534019 BROMODOMAIN-CONTAINING PROTEIN 4 (HUNK1 PROTEIN). [SWISSPROT;Acc:O60885] 0.144761 0.27107837 BRD4
539 0.28704 0.0778103 0.271078247 SRBD1
540 0.13229 0.0358609 0.271077935 LRRC4B
541 0.138821 NAG14 PROTEIN. [RefSeq;Acc:NM_022143] 0.0376313 0.271077863 LRRC4
542 0.561935 PROTEIN REGULATOR OF CYTOKINESIS 1; PROTEIN REGULATING CYTOKINESIS 1. [RefSeq;Acc:NM_003981] 0.152328 0.271077616 no value
543 0.15929 0.0431799 0.27107728 LRRC4C
544 0.36752 TESTIS-SPECIFIC BROMODOMAIN PROTEIN. [RefSeq;Acc:NM_001726] 0.0996239 0.27107069 BRDT
545 2.2133 QUAKING ISOFORM 6. [SPTREMBL;Acc:Q9P0X9] 0.59995 0.271065829 QKI
546 0.183589 ABHYDROLASE DOMAIN CONTAINING PROTEIN 2 (PROTEIN PHPS1-2). [SWISSPROT;Acc:P08910] 0.0497647 0.271065805 ABHD2
547 0.905006 "CUG TRIPLET REPEAT, RNA BINDING PROTEIN 2; ELAV-TYPE RNA-BINDING PROTEIN; CUG TRIPLET REPEAT,RNA-BINDING PROTEIN 2; CUG TRIPLET REPEAT, RNA-BINDING PROTEIN 2; NEUROBLASTOMA APOPTOSIS-RELATED RNA-BINDING PROTEIN. [RefSeq;Acc:NM_006561]" 0.24526 0.271003728 CUGBP2
548 0.986471 CUG TRIPLET REPEAT RNA-BINDING PROTEIN 1 (CUG-BP1) (RNA-BINDING PROTEIN BRUNOL-2) (DEADENYLATION FACTOR CUG-BP) (50 KDA NUCLEAR POLYADENYLATED RNA-BINDING PROTEIN) (EDEN-BP). [SWISSPROT;Acc:Q92879] 0.267337 0.271003405 CUGBP1
549 0.172653 SH3 DOMAIN-BINDING GLUTAMIC ACID-RICH PROTEIN (SH3BGR PROTEIN) (21- GLUTAMIC ACID-RICH PROTEIN) (21-GARP). [SWISSPROT;Acc:P55822] 0.046789 0.271000214 SH3BGR
550 LATS HOMOLOG 1. [RefSeq;Acc:NM_004690] LATS1

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 bloody hugo identifier as demanded by the BMC Bioinformatics idiots
- http://analysis.yellowcouch.org/