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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Rank Gene description measured expected final Hugo
Results: HTML CSV LaTeX Showing element 451 to 500 of 3206 in total
Rank
description
measured
expected
final
Hugo
451 XPA-BINDING PROTEIN 2 (HCNP PROTEIN) (PP3898). [SWISSPROT;Acc:Q9HCS7] 0.441621 1.59982 0.27604418 XAB2
452 "PROTEIN-TYROSINE PHOSPHATASE, NON-RECEPTOR TYPE 1 (EC 3.1.3.48) (PROTEIN-TYROSINE PHOSPHATASE 1B) (PTP-1B). [SWISSPROT;Acc:P18031]" 0.215243 0.779889 0.27599184 no value
453 "PROTEIN-TYROSINE PHOSPHATASE, NON-RECEPTOR TYPE 2 (EC 3.1.3.48) (T- CELL PROTEIN-TYROSINE PHOSPHATASE) (TCPTP). [SWISSPROT;Acc:P17706]" 0.173881 0.6302 0.275913996 PTPN2
454 TRANSDUCIN BETA-LIKE 2 PROTEIN (WS BETA-TRANSDUCIN REPEATS PROTEIN) (WS-BETATRP) (WILLIAMS-BEUREN SYNDROME CHROMOSOME REGION 13 PROTEIN). [SWISSPROT;Acc:Q9Y4P3] 0.132041 0.478695 0.275835344 TBL2
455 MITOCHONDRIAL GTP BINDING PROTEIN ISOFORM V. [RefSeq;Acc:NM_032620] 0.270501 0.981155 0.275696501 GTPBP3
456 0.0394844 0.143261 0.275611646 ZMAT2
457 SQUAMOUS CELL CARCINOMA ANTIGEN RECOGNIZED BY T CELLS 1; U4/U6.U5 TRI-SNRNP-ASSOCIATED 110 KDA PROTEIN; IGE AUTOANTIGEN; SART1(259) PROTEIN; SART1(800) PROTEIN. [RefSeq;Acc:NM_005146] 0.35534 1.28928 0.275611194 SART1
458 ZASP PROTEIN (FRAGMENT). [SPTREMBL;Acc:Q9Y4Z3] 2.49065 9.03714 0.275601573 LDB3
459 COLLAGEN ALPHA 3(IV) CHAIN PRECURSOR (GOODPASTURE ANTIGEN). [SWISSPROT;Acc:Q01955] 0.0421286 0.15287 0.275584484 COL4A3
460 COLLAGEN ALPHA 5(IV) CHAIN PRECURSOR. [SWISSPROT;Acc:P29400] 0.0637349 0.231274 0.27558177699999997 no value
461 TRANSCRIPTIONAL CO-ACTIVATOR WITH PDZ-BINDING MOTIF (TAZ). [RefSeq;Acc:NM_015472] 0.0702636 0.254965 0.275581354 WWTR1
462 9 KDA PROTEIN. [SWISSPROT;Acc:P13994] 0.0869671 0.315578 0.275580364 CCDC130
463 65 KDA YES-ASSOCIATED PROTEIN (YAP65). [SWISSPROT;Acc:P46937] YAP1
464 MITOCHONDRIAL RIBOSOMAL PROTEIN L24. [RefSeq;Acc:NM_024540] MRPL24
465 E1A BINDING PROTEIN P400; P400 SWI2/SNF2-RELATED PROTEIN; CAGH32 PROTEIN; TRINUCLEOTIDE REPEAT CONTAINING 12. [RefSeq;Acc:NM_015409] EP400
466 LIM PROTEIN (SIMILAR TO RAT PROTEIN KINASE C-BINDING ENIGMA); ENIGMA HOMOLOG. [RefSeq;Acc:NM_006457] 1.83106 6.64504 0.275552894 PDLIM5
467 "STERILE ALPHA AND TIR MOTIF CONTAINING 1; STERILE ALPHA AND HEAT/ARMADILLO MOTIF PROTEIN, ORTHOLOG OF DROSOPHILA. [RefSeq;Acc:NM_015077]" 0.305359 1.11055 0.274961956 SARM1
468 GTP-BINDING PROTEIN ERA HOMOLOG (HERA) (FRAGMENT). [SWISSPROT;Acc:O75616] 0.0444465 0.161679 0.274905832 ERAL1
469 "TRIMETHYLLYSINE DIOXYGENASE, MITOCHONDRIAL PRECURSOR (EC 1.14.11.8) (EPSILON-TRIMETHYLLYSINE 2-OXOGLUTARATE DIOXYGENASE) (TML-ALPHA- KETOGLUTARATE DIOXYGENASE) (TML HYDROXYLASE) (TML DIOXYGENASE) (TMLD). [SWISSPROT;Acc:Q9NVH6]" 0.218407 0.794482 0.274904907 TMLHE
470 "PALLIDIN; PALLID (MOUSE) HOMOLOG, PALLIDIN. [RefSeq;Acc:NM_012388]" 0.153744 0.559309 0.274882042 PLDN
471 "CLEAVAGE AND POLYADENYLATION SPECIFIC FACTOR 6, 68 KD SUBUNIT; PRE-MRNA CLEAVAGE FACTOR IM (68KD); CLEAVAGE AND POLYADENYLATION SPECIFIC FACTOR 6, 68KD SUBUNIT; PRE-MRNA CLEAVAGE FACTOR I, 68KD SUBUNIT. [RefSeq;Acc:NM_007007]" 1.05805 3.85379 0.274547913 CPSF6
472 COP9 CONSTITUTIVE PHOTOMORPHOGENIC HOMOLOG SUBUNIT 3; COP9 COMPLEX SUBUNIT 3; JAB1-CONTAINING SIGNALOSOME SUBUNIT 3. [RefSeq;Acc:NM_003653] 0.105796 0.385361 0.274537382 COPS3
473 HEPATOCYTE NUCLEAR FACTOR 3-GAMMA (HNF-3G) (FORKHEAD BOX PROTEIN A3) (FORK HEAD-RELATED PROTEIN FKH H3). [SWISSPROT;Acc:P55318] 0.483455 1.76198 0.274381662 FOXA3
474 SEVEN IN ABSENTIA HOMOLOG 2. [RefSeq;Acc:NM_005067] 0.454535 1.65694 0.274321943 SIAH2
475 PROTEIN SCK (FRAGMENT). [SWISSPROT;Acc:P98077] 0.0379081 0.138197 0.274304797 SHC2
476 NEURONAL SHC. [RefSeq;Acc:NM_016848] 0.0378858 0.138116 0.274304208 SHC3
477 OVARIAN CARCINOMA IMMUNOREACTIVE ANTIGEN. [RefSeq;Acc:NM_017830] 0.126731 0.462009 0.27430418 OCIAD1
478 "SOLUTE CARRIER FAMILY 23, MEMBER 1 (SODIUM-DEPENDENT VITAMIN C TRANSPORTER 1) (HSVCT1) (NA(+)/L-ASCORBIC ACID TRANSPORTER 1) (YOLK SAC PERMEASE-LIKE MOLECULE 3). [SWISSPROT;Acc:Q9UHI7]" 0.0444669 0.162108 0.274304168 SLC23A1
479 SHC TRANSFORMING PROTEIN. [SWISSPROT;Acc:P29353] SHC1
480 DUAL SPECIFICITY MITOGEN-ACTIVATED PROTEIN KINASE KINASE 7 (EC 2.7.1.-) (MAP KINASE KINASE 7) (MAPKK 7) (MAPK/ERK KINASE 7) (JNK ACTIVATING KINASE 2) (C-JUN N-TERMINAL KINASE KINASE 2) (JNK KINASE 2) (JNKK 2). [SWISSPROT;Acc:O14733] 0.209195 0.762639 0.274304094 MAP2K7
481 ADP-RIBOSYLATION FACTOR 3. [SWISSPROT;Acc:P16587] 0.224714 0.819215 0.274304059 ARF3
482 "SOLUTE CARRIER FAMILY 23, MEMBER 2 (SODIUM-DEPENDENT VITAMIN C TRANSPORTER 2) (HSVCT2) (NA(+)/L-ASCORBIC ACID TRANSPORTER 2) (YOLK SAC PERMEASE-LIKE MOLECULE 2) (NUCLEOBASE TRANSPORTER-LIKE 1 PROTEIN). [SWISSPROT;Acc:Q9UGH3]" 0.0377969 0.137792 0.274304023 SLC23A2
483 HETEROGENEOUS NUCLEAR RIBONUCLEOPROTEIN A1 (HELIX-DESTABILIZING PROTEIN) (SINGLE-STRAND BINDING PROTEIN) (HNRNP CORE PROTEIN A1). [SWISSPROT;Acc:P09651] 0.0703022 0.256293 0.274304019 HNRNPA1
484 HETEROGENEOUS NUCLEAR RIBONUCLEOPROTEINS A2/B1 (HNRNP A2 / HNRNP B1). [SWISSPROT;Acc:P22626] 0.0539161 0.196556 0.274304015 HNRNPA2B1
485 0.0257019 0.0936986 0.274303992 CHCHD3
486 ADP-RIBOSYLATION FACTOR 1. [SWISSPROT;Acc:P32889] 0.384939 1.40333 0.274303977 ARF1
487 HETEROGENEOUS NUCLEAR RIBONUCLEOPROTEIN A3 (HNRNP A3) (D10S102). [SWISSPROT;Acc:P51991] 0.0562729 0.205148 0.274303917 HNRPA3
488 ADP-RIBOSYLATION FACTOR 4. [SWISSPROT;Acc:P18085] 0.106754 0.389182 0.274303539 ARF4
489 "ZINC FINGER PROTEIN 289, ID1 REGULATED; LIKELY ORTHOLOG OF MOUSE ZFP289. [RefSeq;Acc:NM_032389]" 0.02648 0.0965355 0.274303236 ZNF289
490 0.0344618 0.125634 0.274303135 CHCHD6
491 ADP-RIBOSYLATION FACTOR GTPASE-ACTIVATING PROTEIN 3 (ARF GAP 3). [SWISSPROT;Acc:Q9NP61] ARFGAP3
492 no value
493 "POTASSIUM CHANNEL MODULATORY FACTOR 1; POTASSIUM CHANNEL MODULATORY FACTOR; DIFFERENTIALLY EXPRESSED IN BRANCHING TUBULOGENESIS 91; ZINC FINGER, ZZ DOMAIN CONTAINING 1. [RefSeq;Acc:NM_020122]" 0.0341617 0.12454 0.274303035 KCMF1
494 FUSED TOES HOMOLOG; LIKELY ORTHOLOG OF MOUSE FUSED TOES. [RefSeq;Acc:NM_022476] 0.277907 1.01314 0.274302663 AKTIP
495 R3H DOMAIN PROTEIN 1. [SWISSPROT;Acc:Q15032] 0.309779 1.12934 0.274300919 R3HDM1
496 MITOCHONDRIAL RIBOSOMAL PROTEIN L18. [RefSeq;Acc:NM_014161] 0.0800469 0.291858 0.274266595 MRPL18
497 0.25596 0.9333 0.274252652 R3HDM2
498 0.236585 0.862726 0.274229593 no value
499 SEVEN IN ABSENTIA HOMOLOG 1. [RefSeq;Acc:NM_003031] 0.563143 2.05361 0.274221006
500 ABL-INTERACTOR 2; ABL-INTERACTING PROTEIN 1 (SH3-CONTAINING PROTEIN); ABL BINDING PROTEIN 3; ARG PROTEIN TYROSINE KINASE-BINDING PROTEIN; ABL-INTERACTOR PROTEIN 2B; SIMILAR TO SPECTRIN SH3 DOMAIN BINDING PROTEIN 1. [RefSeq;Acc:NM_005759] 0.315262 1.14976 0.274198094 ABI2

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/