Decoding ENCODE. Jim Kent University of California Santa Cruz. ENCODE Timeline. ENCyclopedia of Dna Elements. Attempt to catalog as many functional elements in human genome as possible using current technologies. Pilot project - finished 2007, covered 1% of genome.
University of California Santa Cruz
Selected fields from related tables results: Ensemble Gene (ensGene) and Superfamily Description (sfDescription).
681/3329 (20%) of Ensemble not known also not conserved (ensGene) and Superfamily Description (sfDescription).
1728/33,666 (5%) of Ensembl in general not conserved
The family is related in many ways. Sorted by protein homology
of relationships between genes.
genes in a region.
Controlling expression display options.
Column includes 79 tissues, slide only fits first half.
data mining tool.
GO-annotated membrane proteins that are expressed at least 8X in pancreatic islets cells and no more than 4X elsewhere outside of pancreas and central nervous system. These might be good candidates for targets of the autoimmune response that can cause Type I diabetes.
Download via http://genome.ucsc.edu/admin/cvs.html
Many modules require MySQL to be installed.
struct dnaSeq Actual
/* A dna sequence in one-letter-per-base format. */
struct dnaSeq *next; /* Next in list. */
char *name; /* Sequence name. */
char *dna; /* a’s c’s g’s and t’s. Null terminated */
int size; /* Number of bases. */
struct dnaSeq *dnaSeqFromString(char *string);
/* Convert string containing sequence and possibly
* white space and numbers to a dnaSeq. */
void dnaSeqFree(struct dnaSeq **pSeq);
/* Free dnaSeq and set pointer to NULL. */
void dnaSeqFreeList(struct dnaSeq **pList);
/* Free list of dnaSeq’s. */
struct screenObj Actual
/* A two dimensional object in a sleazy video game. */
struct screenObj *next; /* Next in list. */
char *name; /* Object name. */
int x,y,width,height; /* Bounds of object. */
void (*draw)(struct screenObj *obj); /* Draw object */
boolean (*in)(struct screenObj *obj, int x, int y);
/* Return true if x,y is in object */
void *custom; /* Custom data for a particular type */
void (*freeCustom)(struct screenObj *obj);
/* Free custom data. */
#define screenObjDraw(obj) (obj->draw(obj))
/* Draw object. */
void screenObjFree(struct screenObj **pObj);
/* Free up screen object including custom part. */
struct exoFish *exoFishLoad(char **row)
/* Load a exoFish from row fetched with select * from exoFish
* from database. Dispose of this with exoFishFree(). */
struct exoFish *ret;
ret->chrom = cloneString(row);
ret->chromStart = sqlUnsigned(row);
ret->chromEnd = sqlUnsigned(row);
ret->name = cloneString(row);
ret->score = sqlUnsigned(row);
"An evolutionarily conserved region (ecore) with Tetroadon"
string chrom; "Human chromosome or FPC contig"
uint chromStart; "Start position in chromosome"
uint chromEnd; "End position in chromosome"
string name; "Ecore name in Genoscope database"
uint score; "Score from 0 to 1000"
See autoSql.doc for more details.